Fish and Crayfish Completed)

Fishandcrayfishcommunitiesof theBlackwoodRiver:migrations, ecology,andinfluenceofsurface andgroundwater
Prepared for
Prepared by
Fishandcrayfishcommunitiesofthe BlackwoodRiver:migrations,ecology,and influenceofsurfaceandgroundwater

Preparedfor
SouthWestCatchmentsCouncil &DepartmentofWater December,2006
Preparedby
Section1
MigrationpatternsofthefishandcrayfishfaunaoftheBlackwoodRiver
SJBeatty,FJMcAleer&DLMorgan CentreforFish&FisheriesResearch MurdochUniversity SouthStMurdoch WesternAustralia Email:fish@murdoch.edu.au Section2
CrayfishburrowingactivityintheregionoftheYarragadeeDischarge Zone,BlackwoodRiver
AKoenders&PHJHorwitz CentreforEcosystemManagement EdithCowanUniversity 100JoondalupDrive,Joondalup WesternAustralia
Acknowledgements TheauthorswouldliketothanktheSouthWestCatchmentsCouncilandtheDepartmentof Water for funding this study. We would particularly like to thank Rob Donohue, Natasha HydeandAdrianGoodreidfortheirsignificantcontributionsthroughouttheproject.Many thankstoAshRamsey,RichardPickett,andPeterMuirdenfromtheDepartmentofWaterfor providing discharge and water quality data. Thanks also to Joanna HuguesDitCiles from SWCC. We would also like to thank the landholders that allowed us access to their properties,includingShadNixonandRobinMellema,andtoSimonVisser,MarkAllen,Trine Hansen,JoshJohnston,DrewRowland,DamonBrearleyandDoWstaffforhelpinthefield. Thanks particularly to David John for providing accommodation and technical support throughout the project. Most photographs by the authors except Western Hardyhead and FreshwaterCobblerbyMarkAllen.Frontispiece:BalstonsPygmyPerch,PhotoD.Morgan
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Summary
Section1 Migration patterns of the fish and crayfish faunaoftheBlackwoodRiver
SouthwesternAustraliahasahighlyendemicfreshwateraquaticfauna,with 80%ofthefishesand100%ofthecrayfishesfoundnowhereelse.Eachofthe endemic fishes is found within the Blackwood River catchment, with two beingrestrictedtothefloodplainsoftheScottRiver;amajortributaryofthe Blackwood. Salinisation of the catchment has compromised the natural rangesofmanyofthefishes,withmanyofthenonhalotolerantspeciesnow restrictedtoforestedtributarieswithinthelowercatchmentandinthesection ofthemainchannelwheresalinityisreducedasaconsequenceofdischarge fromtheYarragadeeandLeedervilleaquifers. Prior to this study, only snapshot fish surveys around the major regions of LeedervilleandYarragadeegroundwaterdischargeintotheBlackwoodRiver existed allowing only a limited understanding of the ecology of the fish communities and their relationship with key environmental variables; particularly surface and groundwater hydrology. This knowledge is important in the light of potential future increased groundwater extraction andclimatechange.Tofurthertheunderstandingofthefishcommunitiesof thisregion,Section1ofthisstudyexaminedthetemporalmigrationpatterns of fish and freshwater crayfish in this zone of the Blackwood catchment. Specifically, upstream and downstream migration patterns of fishes in the BlackwoodRiveranditstributarieswereexaminedandrelated toanumber of key environmental variables, such as surface and groundwater discharge. Predictions of the effects on fauna by projected changes in environmental variables,forexample,duetoaquiferdrawdown(e.g.reduceddischargeand increasedsalinity)wereexamined. Inordertodeterminefishmigrationswithinandoutsideofthemajorareaof groundwater discharge, four main channel sites (one receiving the entire Yarragadee discharge, one at the upstream point of the discharge, and two upstream of the discharge) were monitored. Furthermore, sites within four tributarieswerealsomonitoredforpatternsoffishmigrationandcommunity structureinrelationtoenvironmentalvariables;namelysurfacewaterreliant seasonal systems, i.e. Rosa Brook, Layman Brook and McAtee Brook, and a perennial groundwater fed system, i.e. Milyeannup Brook. Migration and populationdemographicswereexaminedoneightoccasionsbetweenOctober 2005 and September 2006. A variety of sampling methods were utilised includingfykenetting,seinenetting,trappingandelectrofishing.
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Substantial differences in fish densities and migration patterns existed between and within the main channel and major tributaries. The main channel was dominated by estuarine and salttolerant species at all sites. However, main channel sites receiving most groundwater discharge (i.e. receiving both Leederville and Yarragadee Aquifer discharge) had much greater abundances of nonsalt tolerant freshwater native species than those sitesupstreamoftheYarragadeedischarge.Thissuggeststhatalthoughthe fish community in the main channel may have changed to primarily salt tolerantspeciesinresponsetoincreasingsaltlevels,freshgroundwaterinput insummer(whenmanytributariesceasetoflowordrycompletely),maybe enablingthosespeciestocontinuetosurviveinthemainchannel. ThestudyalsorecordedaconsiderableupstreammigrationoftheFreshwater Cobbler at all main channel sites in spring and summer; a period that coincided with their spawning. It was found that upstream Freshwater Cobbler migrations in main channel sites were highly correlated to summer discharge.Thisspeciesisconsideredtobeidealforlongtermmonitoringof riverconnectivity. The Marron population was assessed in the main channel and a slightly higherrelativeabundance(althoughnotstatisticallysignificant)wasrecorded withinsites receivingmostgroundwaterdischarge(i.e. bothLeedervilleand Yarragadee Aquifer discharge) than those upstream. Marron catches have recently been found to be positively correlated with river flow and this has implications for the recreational fishery within the Blackwood River under reducedflowscenarios. Considerabledifferencesinthetimingandstrengthsoffishmigrationswere recordedbetweentributariesfortheWesternMinnow,NightfishandWestern Pygmy Perch, that utilised all four tributaries to varying degrees. It was foundthatthetributariesactasthemajorspawninghabitatsforthesespecies and the section of the main channel that receives the most groundwater discharge acts as a refuge to the summer contraction or drying of most of thesesystems. Significantdifferencesinstrengthofmigrationsbetweentributariesforsome native freshwater species wereexplained by environmentalvariablesduring the peak flow period. For example, downstream and upstream migration strengths of the Western Minnow in the four tributaries were highly correlated with stream discharge whereas upstream migrations of Western PygmyPerchandNightfishwerecorrelatedwithdissolvedoxygenlevelsand earlierbreedingandrecruitmentofWesternMinnowsoccursintheperennial MilyeannupBrook.
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Milyeannup Brook is one of only two (along with Poison gully) perennially flowingtributariesinthisregionoftheBlackwoodandaredirectlyrelianton Yarragadee Aquifer discharge. It was apparent that this system is of critical conservation importance as it houses the only population of the Balstons Pygmy Perch in the Blackwood River catchment (listed as Vulnerable under the EPBC Act 1999). This study found a clear upstream and downstream spawningmigrationofBalstonsPygmyPerchinthissystemandfoundonly limitedupstreammovementfromthemainchannelsuggestingitisacrucial refuge to Balstons Pygmy Perch in the Blackwood River catchment. By mappingfishdistributionsalongitslength insummer,thestudyalsofound thatBalstonsPygmyPerchonlyutilisedthelower~1300mofthe~2500mbase flowstreamlengthsuggestingthatonly~52%containedsuitablehabitat(e.g. adequatedepth)foroccupation.Theminimumpopulationofthisspeciesin this system was found to be ~380 42 fish based on their density. This low population minimum makes this species particularly vulnerable to potential habitat decline; particularly if main channel summer water quality decline exceedsthisspeciesenvironmentaltolerance. A number of key knowledge gaps pertaining to the ecology of the fish communitiesareidentified. Majorknowledge gapsincludedetermining the degreeofinterannualvariationingroundwaterrelianceofthesecommunities, salinity tolerances of these species,andidentifyingcriticalriffle zones inthe BlackwoodRiverthatareimportantinmaintainingriverconnectivity.
Section2
Crayfishburrowingactivityintheregionofthe YarragadeeDischargeZone,BlackwoodRiver
Astudyoftheburrowingactivityoffreshwatercrayfishintheregionofthe Yarragadee Discharge Zone was conducted over the period of one year, starting September 2005. The aims of the study were to determine seasonal effects on burrowing activity for freshwater crayfish species in response to groundwater and surface water changes, and to relate these to emergent crayfish. In addition, a pilot study of the chemical characteristics of surface andgroundwaterintheareawasundertakentodetermineifdischargefrom the Yarragadee was detectable and if it was a migratory cue for freshwater crayfish. TransectsweresetupincreeksreceivinginputfromtheYarragadee(Layman Brook, Poison Gully and Milyeannup Brook), as well as in control sites upstream(McAteeBrook)anddownstream(RosaBrook).Burrowingdensity andactivityweremonitoredfromOctober2005toSeptember2006,aswellas basic surface water and groundwater physicochemistry. In addition, observationsweremadeofemergentcrayfishduringthedayandatnight. The study area appears to be typical burrowing habitat for southwestern Australianfreshwatercrayfish.Fourspeciesoffreshwatercrayfishwerebeen identified:Marron(Cheraxcainii),Gilgie(C.quinquecarinatus),RestrictedGilgie (C.crassimanus)andKoonac(C.preissii).Burrowsandburrowingactivitywere highlyseasonalandprovidebaselinedataonfreshwatercrayfishresponsesto declinesinsurfaceandgroundwater. The very dry autumn and early winter experienced in 2006 resulted in a slower than usual recovery of water levels (i.e. water levels experienced in September 2005 were much higher than those found in the corresponding monthin2006).Whilesomemethodologicalproblemswereencountered(i.e. species specific burrowing behaviour could not be discerned), some generalisationsarepossible,including: - burrowing activity increases in response to receding water levels/tables; - thedepthtowhichcrayfishburrowcanbegauged,atleastin,partby thenatureofthesoilextrudedfromtheburrow; - ephemeraltributariesmay beimportantforbreeding (i.e.forGilgies); andGilgiesmayhaveanupstream(outofmainchannel)migrationfor breedingandreleasingjuveniles; - smaller Marron individuals use permanent flows out of the main BlackwoodRiverchannel;
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Koonacsaremorelikelytooccurinhabitatswithadeeperreachtothe watertable; the Restricted Gilgie may have resident populations in the two permanent streams receiving Yarragadee discharge throughout the year.
Future monitoring of transects or other sites can test the following hypotheses: A. If groundwater decline in Milyeannup Brook and Poison Gully is extending beyond historical ranges then the burrowing activity of freshwater crayfish will produce soil from a lower stratigraphic soil layer than previously observed. B. If groundwater decline is extending beyond historical ranges, then periods of burrowing activity will occur earlier in spring, and burrows will open later in the autumnorwinter. Water samples were also collected in November/December 2005 before surface waters had receded, where the influence of groundwater discharge wasrelativelyminimal,andinMarch2006whengroundwaterdischargewas a more significant contributor to surface waters. The elemental suites of samples from transect surface waters, and other selected sites were determined. The pilot study of elemental water chemistry demonstrated the potential for characterising the Yarragadee discharge. In addition, high S:(Ca+Mg) ratios in Poison Gully and Milyeannup Brook indicate poor buffering and, if confirmed, may show potential for acidification should sedimentsbecomeexposedduetodroughtand/orgroundwaterdecline.
Contents
Summary...............................................................................................................3 Contents................................................................................................................8 Section1Migrationpatternsoffishandcrayfishfauna oftheBlackwoodRiver...
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Background.............................................................................................................11
FishandfreshwatercrayfishesoftheBlackwoodRiver...11 Importanceofgroundwatertoaquaticfauna.. 12 GroundwatercontributionstoBlackwoodRiverflow.... 13 MilyeannupBrookandPoisonGully..... 14 Aimsofthestudy... 14
Methodology...........................................................................................................15
Studysiteselection...15 Waterqualitymonitoring...17 Fishandcrayfishmonitoringprotocols....... 20
Resultsanddiscussion......................................................................................... 25
Waterqualityinthemainchannelandtributaries.... 25 Speciescapturesummary.....34 FreshwaterCobbler..... 36 WesternMinnow.....45 MudMinnow......56 BalstonsPygmyPerch....59 WesternPygmyPerch.....63 Nightfish......71 SouthwesternGoby.....79 SwanRiverGoby.....84 WesternHardyhead.....88 PouchedLamprey.....94 EasternMosquitofish..... 97 Goldfish....... 100 RainbowTrout.....101 Marron.....103 Gilgie....... 111 RestrictedGilgie......114 Koonac........ 116 MilyeannupBrookCasestudy.....118
Conclusionsandrecommendations...................................................................127
References...............................................................................................................129
Appendices............................................................................................................. 132
Section 2 Crayfish burrowing activity in the region of YarragadeeDischargeZone,BlackwoodRiver... 140
Aimsandobjectives........................................................................................141
Crayfishburrowing...........................................................................................142
Methods....................................................................................................................142
Transectestablishmentanddesign....142 Watercharacteristics.... 42 1 Crayfishburrowmonitoring...144
Results.......................................................................................................................146
Transectdata.... 146 BlackwoodRiverStPatricksElbow.....146 LaymanBrookLaymanRoad........147 LaymanBrooktributaryLaymanRoad....148 LaymanBrookCrouchRd........ 149 MilyeannupBrookHelyarRd........151 MilyeannupBrookMilyeannupRd..152 McAteeBrookCrouchRd.........153 McAteeBrooktributaryCrouchRd.. 54 1 PoisonGullyBlackwoodRd..156 RosaBrookCrouchRd..157 RosaBrooktributaryCrouchRd... 59 1 RosaBrookheadwaterMowenRd....160 RosaBrookgullyMowenRd....161 Transectcomparisons...... 162 Burrowingactivityandmigratorybehaviourofspecies... 164
Discussionandrecommendations..... 166

Waterchemistry.................................................................................................168
Introduction...........168 Methods.................. 168 Results............. 169 Discussionandrecommendations......171 Appendices.........174
Section 1
Migrationpatternsofthefishandcrayfishfaunaof theBlackwoodRiver

SJBeatty,FJMcAleer&DLMorgan
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BACKGROUND
FishandfreshwatercrayfishesoftheBlackwoodRiver
ThefishfaunaoftheBlackwoodRivercatchmentwasdocumentedinMorgan etal.(1998,2003)andthereareadditionalrecordsofthefishesintheWestern Australian Museum collections and in the unpublished literature. These includeabaselinestudyonfishesintheYarragadeeAquiferDischargeZone (hereafter named YADZ) by Morgan & Beatty (2005) and by CENRM (2005) andastudyonRosaBrook(Morganetal.2004).Distributionalinformationon freshwater crayfish in the region is detailed in Morrissy (1978), Austin & Knott(1996),Horwitz&Adams(2000),Nickoll&Horwitz(2000),Morganet al.(2004a)andMorgan&Beatty(2005). Ofnoteisthefactthatalleightspeciesoffreshwaterteleostthatareendemic to southwestern Western Australia are found within the Blackwood River catchment(Morganetal.1998,2003).Salinisationthroughoutbothmostofthe upper catchment and the main channel has led to a decline in the range of manyofthesaltintolerantfishesandmuchoftheuppercatchmentandmain channel is dominated by salttolerant species (Morgan et al. 2003). Thus, salinisationofthecatchmenthasseenmanyofthespeciesthatarenottolerant tohighersalinitylevelsbecomerestrictedtotheforestedsectionsoftheriver that receive discharge from sources such as the Leederville Aquifer and YarragadeeAquifer(Morganetal.2003,Morgan&Beatty2005).Thereislittle historical information on the fish and freshwater crayfish fauna of the receivingenvironmentsurroundingtheYarragadeedischargearea,however, CENRM (2005)recorded amaximumoffournativeandoneintroducedfish speciesfrom19mainchannelsitesandamaximumofthreenativefishspecies from13tributarysitesfromsamplingduringJuly2004.Incontrast,Morgan & Beatty (2005) found nine native and two introduced fish species from six mainchannelsitessampledandninenativeandtwointroducedfishspecies from 21 tributary sites in this area of the catchment. Differences in the diversity expressed in the above studies is likely to be a consequence in the former study conducting sampling during winter when water levels were higherandthusspeciesdensitiesreduced,whilethelatterstudy(i.e.Morgan &Beatty2005)sampledduringautumnwhenwaterlevelswereataminima andthusdensitiesoffisheswererelativelyhigh. Morgan&Beatty(2005)foundasignificantdifferencebetweenthefishfauna associated with main channel sites when compared to tributaries and there were substantial differences in the main channel fauna upstream and downstreamoftheYADZ.Forexample,sitesdownstreamoftheYADZhada muchhigherdiversityoffishandfreshwatercrayfishthanmainchannelsites upstream of the discharge area. Thus, within the main channel sites that
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receivesummerinputfromtheYarragadee,11speciesoffishandfourspecies crayfish were captured compared to four species of fish and two species of crayfishupstreamofthedischargezone.Furthermore,thefourspeciesoffish in the main channel in the upper riverine part of the study area were all halotolerant,whereasmostoftheadditionalspeciespresentinthesitesinthe lowersectionoftheriverarethoughttotolerateonlyrelativelylowsalinities. Anumberofspeciesfoundinthemainchannelaregenerallyabsentfromthe tributary sites sampled and vice versa. For example, Freshwater Cobbler (Tandanus bostocki), Western Hardyhead (Leptatherina wallacei), Swan River Goby(Pseudogobiusolorum)andSouthwesternGoby(Afurcogobiussuppositus) were all predominantly captured in the main channel, while Mud Minnows (Galaxiella munda) and Balstons Pygmy Perch (Nannatherina balstoni) were restricted to tributaries and, in the case of the latter species, to essentially a singletributary. Of the fish species known from the Blackwood River catchment: four are listed on the Australian Society for Fish Biologys List of Threatened Fishes, whileone,BalstonsPygmyPerchhasrecently(2006)beenlistedasVulnerable undertheEPBCAct1999,and,alongwiththeMudMinnowisalsolistedas Schedule1byCALMundertheWildlifeConservationAct1950.Theseendemic fisheshaveundergonemassivereductionsintheiroverallrangeoverthelast 100years(Morganetal.1998),largelyasaresultofmodificationofhabitats, with salinisation of the major catchments a key threatening process (see Morganetal.2003). The 11 species offreshwater crayfishes ofWesternAustraliaareall endemic to the southwest region. Six of these belong to the genus Cherax, and although this is the most widely distributed freshwater crayfish genus in Australia, the native Western Australian Cherax species have been shown to be monophyletic probably due to the long period of separation of south western Australia to the rest of the continent (Crandall et al. 1999). The remaining five native species of freshwater crayfish in Western Australia belong to the endemic genus Engaewa, with Horwitz & Adams (2000) proposing that Engaewa reducta, E. pseudoreducta and E. walpolea fulfil the IUCN criteria to belisted asEndangered,CriticallyEndangeredand Vulnerable, respectively.
Importanceofgroundwatertoaquaticfauna
Groundwater has been estimated to account for between 30 and 70% of the worldstotalfreshwater,withsurfacewaterssuchasriverscontaining<0.01% (Freeze & Cherry 1979, Petts et al. 1999). Many rivers are classified as groundwaterdependent ecosystems, and are further characterised by the
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degree of dependency on groundwater (Boulton & Hancock 2006). Groundwaterdependent ecosystems are complex, often support a relatively diverse fauna and may provide refugia for relictual species, however they vary in their degree of dependency on groundwater to maintain their compositionandfunction(Hattons&Evans1998,Poweretal.1999,Murrayet al.2003,Humphreys2006).Localisedareasofgroundwaterwaterdischarge into streams creates a unique environment known as the hyporheic zone. Characteristics of this region are important in maintaining populations of aquatic species, including fish. For example, the hyporheic zone often provides a thermal refuge for aquatic species by buffering against extreme upper and lower lethal temperatures (Power et al. 1999, Hayashi & Rosenberry 2002). The hyporheic zone influences water quality by maintaining flows independent of surface runoff, supplying dissolved oxygen, maintaining stream productivity, and providing habitat and maintainingmigratoryroutes.Thereareanumberofspecificexamplesthat document the importance of groundwater to particular species in particular systems, however, Sear et al. (1999) considered that the nature of the importance of groundwater is difficult to determine at a regional scale, but shouldbeassessedatalocalorcatchmentlevel. Amajoraimofthestudywastodeterminetherelationshipbetweenfishand freshwater crayfish communities and environmental variables within the BlackwoodRiver;includingdegreeofgroundwaterdependency. GroundwatercontributionstoBlackwoodRiverflow The Yarragadee Aquifer groundwater currently discharges into the Blackwood River in the reach just downstream of Laymans Brook to just upstream of Milyeannup Brook (Figure 1). Although the Yarragadee groundwater discharge contributes only ~1% of the 940GLyr1 of the annual Blackwood River discharge during the dry months, groundwater from the Yarragadee and Leederville Aquifers contribute to between 30100% of the dischargedependingontheamountofsummerrainfall(Strategen2006).This groundwaterdischargeeffectivelydilutesthesalinityoftheriverduringdry months. However,whenthewinterpeakdischargemovesthroughthemainchannel, theelevatedsalinitiesareexperiencedasthewaterflushesdownsaltfromthe uppercatchment(seeResults).Atthistime,thefreshwatertributariesofthe lower, forested Blackwood River are flowing and thus act as refuges for freshwater native fish species (Morgan et al. 2003, Morgan & Beatty 2005). However, in summer, many of these tributaries (aside from Milyeannup Brook and Poison Gully which are perennial due to Yarragadee Aquifer discharge)ceasetofloworeitherdrycompletelyorbecomepools,resultingin
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the freshwater native fish moving into the main channel in the Yarragadee Aquifer discharge zone. A previous study by Morgan & Beatty (2005) revealedthatmostofthesespecieswereabletoexistinthisdiluteddischarge zone in the main channel during summer yet were not found in significant numbersupstreamofthatzone. MilyeannupBrookandPoisonGully Asmentioned,MilyeannupBrookandPoisonGullyaretheonlypermanently flowingstreamsinthisregionoftheBlackwoodRiver.Theirbaseflows(dry period)aremaintainedbydirectdischargefromtheYarragadeeAquifertoa distanceof~2500and3500mfromtheirconfluencewiththemainchannelof theBlackwoodRiverduring2006.MilyeannupBrookhasarelativelydistinct channel form whereas Poison Gully is more diffuse with a lower gradient creating almost a wetland appearance in some sections. Due to the reliance ongroundwaterforpermanency,watertablereductioninthelowersections of both Milyeannup Brook and Poison Gully would reduce baseflow dischargeandalsostreamlength(Strategen2006).
Aimsofthestudy:
Theoverallaimofthestudywastorelatepatternsoffishandcrayfish migrationstoprevailingenvironmentalvariablesintheBlackwoodRiver. Specificaimswereto: Comparethepopulationdemographicsandmigrationsofthefish andfreshwatercrayfishfaunawithinareasoftheBlackwoodRiver main channel that receive major groundwater discharge to those upstreamsitesthatdonot. Describethepopulationdemographicsandmigrationsofthefish andfreshwater crayfishfaunaassociatedwithin thetributariesof the Blackwood River within the Yarragadee Aquifer discharge zone (i.e. Milyeannup Brook, Poison Gully and Layman Brook) and compare these to adjacent tributaries that are not fed by this aquifer(i.e.RosaBrookandMcAteeBrook). Determine seasonal changes in key environmental variables withintheabovetributariesandintheBlackwoodRiver. Identify relationships between migration patterns, population demographicsandthekeyenvironmentalvariables. Gather a comprehensive seasonal baseline dataset of the patterns of fish and crayfish movements in the Blackwood River to allow ongoing monitoring of potential biotic changes that may result frompredictedalterationstothecurrenthydrologicalregimes.
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METHODOLOGY
Studysiteselection
BlackwoodRivermainchannel Site selection for determining the temporal changes in population demographicsandmigrationsofthefishandcrayfishfaunaintheBlackwood Rivermainchannelwasbasedontheirdifferingproximitiestothemajorzone ofgroundwaterdischarge.Forexample,thefishfaunafoundwithintwosites intheBlackwoodRivermainchannelthatissubjectedtothemajordischarge of ground water (from the Yarragadee Aquifer) was compared to two sites upstreamofthisdischarge. The two sites within the main channel that receive groundwater input were immediately downstream of the mouth of Milyeannup Brook (34.0909oS 115.5661oE) and just upstream of the mouth Rosa Brook (34.1081oS, 115.4505oE). The two upstream sites include Jalbarragup Road crossing (34.0421oS,115.6025oE)andQuigup(33.9736oS,115.7008oE)(seeFigure1). Sampling was conducted in October, November and December 2005 and February, March, June, August and September 2006. See page 20 for the biologicalsamplingregime. BlackwoodRivertributaries Milyeannup Brook and Poison Gully are directly maintained in dry months by groundwater discharge. Layman Brook receives groundwater discharge during winter and spring but not summer; when it ceases to flow. The temporalchangesinthepopulationdemographicsandmigrationsofthefish andcrayfishfaunawithinthesetributarieswerecomparedwithtwoadjacent tributariesthatflowseasonally,i.e.RosaBrookandMcAteeBrook;withinthe LeedervilleAquiferdischargezone.
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Seine/electrofishing tributary sites Tributary fyke net sites Main channel sites
Quigup
McAtee Bk
Rosa Brook
Layman Bk
Jalbarragup Milyeannup Pool

Milyeannup Brook Poison Gully
Denny Rd
Figure1
SamplingsitesinthemainchannelandtributariesoftheBlackwoodRiver.
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Waterqualitymonitoring
In order to characterise the climatic regime during the sampling period, relative to the historical climate of the region, rainfall and temperature data were obtained for the Australian Bureau of Meteorology for Bridgetown; a locationforwhichlongtermdatawereavailable.Thisisimportantasithas implications in terms of the appropriateness of the biological data as a baseline and for understanding interannual variations in future monitoring programs. Inordertogainamorepreciseunderstandingoftemperatureregimesofthe various tributaries sampled in this study, temperature data loggers (TinytagTM)wereplacedinsituintomigrationsamplingsitesinthetributaries (Figure 1) and programmed to log temperature every three hours. Temperature loggers were also put in situ at the Blackwood River main channel sites. Data from the loggers were downloaded and temperature regimesofthevariousaquaticsystemsweregraphicallycompared. On each sampling occasion at each site, the temperature (in addition to the temperature data loggers), conductivity, pH, and dissolved oxygen were obtainedfromthemiddleofthewatercolumnatthreelocationsateachsites andamean(1SE)determined. MonthlydischargeestimatesineachtributarysiteweretakenbyDepartment ofWater(Bunburybranch)staffattheapproximatetimesthatsamplingtook place for fish migrations. Main channel discharges were obtained from the DepartmentofWatergaugingstationsatNannup(approximatingtheQuigup sampling site), Darradup (upstream of the Yarragadee discharge, approximatingJalbarragupsamplingsite),Gingilup(receivingthemajorityof theYarragadeedischargeinthemainchannel,approximatingtheDennyRd samplingsite).ThemonthlydischargefortheMilyeannupPoolsamplingsite (at the uppermost point of the Yarragadee discharge) was estimated as the averageofthemonthlyDarradupandGingilupdischarges(seeFigure2).
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1.0 0.9 0.8 0.7
Lower Blackwood River 609-1362
Hut Pool
Gingilup
Poison Confl
Sues Bridge
Layman Brook
Flow (m3/s)
Milyeannup Confl
0.6 0.5 0.4 0.3 0.2 0.1 0.0
Dist from Molloy Is. (km) Flow (Mar2003) Flow (Mar2004) Flow (Feb2005) Flow (Mar2006) "Limits Baseflow LBF (Mar2006) LBF (Mar2003) LBF (Mar2004) LBF (Feb2005)
Darradup
40
50
60
70
80
90
100
110
120
Figure2
Snapshot of discharge within the study area in March 2003, 2004, 2005 and 2006. N.B. vertical dotted lines approximate Yarragadee Aquifer discharge boundaries.FigurebyDepartmentofWater,Bunbury.
Determiningkeyenvironmentalvariablesformigrationstrengthsdata analysis The relationships between the strength of native fish migrations in the tributaries and the main channel and key environmental parameters were examinedviaregressionanalyses.Fortributaries,thenativespeciesincluded in analyses were those where adequate migration data were recorded (i.e. utilised the most number of tributaries) and included the Western Minnow, Western Pygmy Perch, and Nightfish. For the main channel, the analysis focused on the Freshwater Cobbler, which was captured in the greatest numbersatallsites. Inordertoexaminewhichoftheenvironmentalvariablesbestexplainedthe variability in migration strengths in tributaries, the mean number (standardised to 100 % of stream width) of the above species captured in upstream and downstream fyke nets during the major flow and breeding periods (i.e. the period that all four tributaries were flowing significantly, August to December) was determined for each tributary. Subsequently, correlationanalysesandstepwisemultipleregressionmodelsweredeveloped todeterminewhichsingleorcombinationsofenvironmentalvariablesduring
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this major flow and/or breeding period explained the most variation in upstreamanddownstreammigrationsofthosespecies. WithinthemainchanneloftheBlackwoodRiver,theassociationbetweenthe strength of upstream and downstream Freshwater Cobbler movements and the above key environmental variables (with discharge data obtained from the Department of Water gauging stations at Nannup, Darradup and Gingilup)weresimilarlyexamined.Firstly,allsamplingoccasionsatallsites were included in stepwise regression analysis to determine which of the environmentalvariablesexplainedthevariationin upstream ordownstream Freshwater Cobbler movements in the Blackwood River. Secondly, overall mean upstream and downstream Freshwater Cobbler movements in each of the four main channel sites, pooled for the major migration period (i.e. betweenNovemberandJuly),werecorrelatedwiththeaboveenvironmental variables during that period to determine which, if any, accounted for the observeddifferencesinmigrationstrengthsbetweenthosesites. For the above analyses, ShapiroWilk statistical tests for normality were undertaken for each variable and all data were subsequently log10 transformed prior to analysis. Bivariate correlations between each environmental variable were calculated (Pearsons correlation coefficient) prior to each stepwise regression analysis to initially examine relationships between environmental variables. Mean velocity was consistently highly correlated with discharge and was therefore excluded from the analyses to avoidproblemswithcolinearity. Inthesubsequentstepwiseregressionanalyses,levelsofcolinearitybetween independent variables were investigated via determining condition indexes and eigenvalues. The more conservative, adjusted coefficients of determination(r2)wereexaminedineachmodelastheadjustedvaluesclosely reflect the goodness of fit of the model. The significance of the models are alsopresented(pvalues)(SPSS,2005). It should be noted that only a limited number of tributaries and variables wereexaminedintheregressionanalysesandthereforethemodelsgenerated should be viewed as highlighting apparent trends in the relationships between the limited number of environmental variables and migrations of each species and not precise predictive tools as is often the case with larger datasets.Furthermore,therearemanyotherhabitatdifferencesbetweensites thatwouldalsoexplainvariationinfishmovementsbetweenthesesitesand systems that were not examined. However, the environmental associations describedherearenonethelesssignificantfromastatisticalperspective.
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Fishandcrayfishmonitoringprotocols
A number of techniques were employed to examine the fish and crayfish faunaofthemainchannelandtributarysitesintheBlackwoodRiver(Figure 3).Eachmethodisoutlinedbelow,i.e.theuseoffykenets(11.2minwidth, includingtwo5mwingsanda1.2mwidemouthfishingtoadepthof0.8m, 5mlongpocketwithtwofunnelsallcomprisedof2mmwovenmesh);seine nets(5,10and15mnetscomprisedof2mmwovenmesh;anda26mseine netconsistingoftwo9mwingsof6mmwovenmeshandan8mbuntof3 mmmesh);240and12velectrofishers;andcrayfishtraps. BlackwoodRivermainchannel Speciesmigrations At the four main channel sites (see Figures 1 and 3), fyke nets were used to determine temporal trends in species migrations. Fyke nets were set facing upstream, to determine downstream movements of fish, and facing downstream, to determine upstream movements of fish. Each fyke net was setforaperiodof24hwiththreereplicatestakenoneachsamplingoccasion. Each fish and freshwater crayfish captured was identified, a subsample measured (total length (TL) for fish and orbital carapace length (OCL) for crayfish) to the nearest 1 mm and where possible sexed and released. A subsampleofmostspecieswasretainedforanalysesofbiologicalindicessuch as gonadal development and aging, some of which are provided in this report,butmostofwhicharetobeinvestigatedfurther. Duetothehighvolumeofwaterandlargewidthofthemainchannelitwas rarely possible to completely block the main channel sites and therefore capture all fish moving upstream or downstream past a point at the site. Therefore, the mean number of each species captured on each occasion was adjusted to account for total number of each species migrating through a section of the river. For example, if our fyke nets blocked 90% of the main channel and we caught 90 fish, this would be adjusted by 100/90 to account forallfishmovingpastthispointintheriverandthuswewouldestimatethat in fact 100 fish swam through this section of the river over the 24 h period. The total numbers referred to here on in are the actual numbers captured, whilethegraphsreflecttheadjusteddatatoshowtheapproximatenumbers of fish actually migrating and to thus allow for comparisons between the variousriverinereaches.
20

Figure3 Fykenetssetin(A)themostupperBlackwoodRivermainchannelsite,i.e. Quigup, (BC) Jalbarragup, (DE) upstream of Rosa Brook (Denny Rd), and (F)MilyeannupPooldownstreamofMilyeannupBrookmouth.
Speciesabundances Replicate sampling over a given area (m2) using seine netting and/or electrofishingwasusedtodeterminetherelativeabundancesofthedifferent species in the different main channel sites. All fish and freshwater crayfish captured were identified, a subsample measured and the majority released, although a subsample was often retained for biological analyses (e.g. for maturitydataandlengthatage). Relative crayfish abundances were determined using up to 13 crayfish traps setovernightateachmainchannelsiteoneachsamplingoccasion.Themean numbercapturedateachsitewascomparedusingANOVA.
21
BlackwoodRivertributaries On each sampling occasion (if the system was flowing), fyke nets were set over three days and nights in Milyeannup Brook (2 sites), Layman Brook, RosaBrookandMcAteeBrook(Figure4).Ateachsite,onenetwassetfacing upstream,tocapturefishthatwere moving downstream,whileanother was set facing downstream (to capture fish moving upstream) and each was checked every 24 h (Figure 4). As with the main channel site captures, the percentcoverageofeachsetwasdeterminedandthecatcheslateradjustedto 100%ofthestreamwidth.

Figure4 Fyke nets set in (A) upper Milyeannup Brook (Blackwood Rd), (B) lower MilyeannupBrook,(C)MilyeannupBrookmouth,(D)LaymanBrook(Denny Rd),(E)RosaBrook(DennyRd),and(F)McAteeBrook.
22
Theshallow,diffusenatureofPoisonGullyprohibitedeffectivesamplingfor fish migration; therefore, a seasonal quantitative analysis of the fish and freshwater crayfish was undertaken using a backpack electrofisher. Three replicate density estimates were taken with up to 90 m2 sampled on each occasion. In addition, electrofishing was employed in October 2005 in McAtee, Rosa and Layman Brooks and again in December 2005 in McAtee Brooktoexaminespeciesdemographics.Regardlessofcapturemethod,fish species were identified, with a large subsample measured for total length (mm TL) for fish and orbital carapace length (mm OCL) for freshwater crayfishandbeforebeingreleased.Thosenotmeasuredwereidentifiedand counted to determine total numbers. A small subsample of native species wasretainedforbiologicalinvestigationintothegonadaldevelopment(upto ~30permonth)andforfuturegeneticanalysis. Freshwatercrayfishwereidentified,measuredtothenearestmmOCL,sexed and released. A small number were retained for determination of size at sexualmaturity. Marronpopulationanalysis Samplingregime In order to compare the relative abundances of Marron at sites within the mainchanneloftheBlackwoodRiver,samplingforMarronoccurredatatotal of six sites in the Blackwood River on seven sampling occasions; correspondingwiththefishmigrationsampling.Inadditiontothefoursites sampled for fish migrations, an additional two were selected (near the confluence of Red Gully, upstream of the YADZ, and near the entrance of Laymans Brook, at the most downstream point of the YADZ) in order to sample a greater range of representative habitats within and outside of the major zone of groundwater discharge to avoid potential bias resulting from accessibilitybyrecreationalfishers(Figure2). On eachsamplingoccasion,upto13 boxstylecrayfishtraps were deployed overnightspacedapproximately15mapart.Trapswerebaitedwithpoultry pellets. Upon retrieval, all crayfish were identified, sexed and measured to thenearest1mmorbitalcarapacelength(OCL).MaleMarronwerereleased atthesiteofcaptureandasampleoffemaleswereeuthanasedbyimmersion in an ice slurry and later examined for determination of reproductive stage. FemaleMarronweredissectedinthelaboratoryandeachindividualassigned anovariandevelopmentalstageaccordingtoBeattyetal.(2003). Dataanalysis Thecatchperuniteffort(CPUE)ofMarrononeachsamplingoccasionateach sitewasdeterminedbycalculatingthemeannumberofMarroncapturedper
23
trappernight.ThestatisticalsignificanceofCPUEwastestedusinggeneral linear models (ANOVA) with Levenes test of homogeneity of variance first beingconductedanddatabeinglogtransformedwhennecessary. In order to compare population structures of Marron in the sites receiving YADZ (i.e. Milyeannup Pool; near the Laymans Brook confluence, and at DennyRoad;neartheRosaBrook confluence) tothosesites upstreamofthe zone (i.e. near the confluence of Red Gully, Jalbarragup Road crossing, and Quigup), lengthfrequency distributions over the sampling months were producedforeach ofthetwozones.ThemajorspawningperiodofMarron was determined by examination of the temporal pattern in proportions of femaleovarianstages(seeBeattyetal.2003,2005). The OCL at which 50 (L50) and 95% (L95) of female Marron mature in the BlackwoodRiverwasdeterminedbyundertakinglogisticregressionanalysis ofthepercentagecontributionsmadetoeachlengthclassbyindividualsthat containeddeveloping/maturegonads(stagesIIIVII).Datawererandomly resampled and reanalysed to create 500 sets of bootstrap estimates. The logisticequationis: POCL=1/[1+eln19(OCLOCL50)/OCL95OCL50)] where POCL is the proportion of Marron with mature gonads (see below) at lengthintervalOCL.OnlythoseindividualscapturedinJulyandAugust(i.e. immediatelypriortoandthroughoutthe breeding period, see Results)were usedintheanalysis(forfullmethodologyseeBeattyetal.2004). FreshwaterCobblerpopulationanalysis In order to further examine patterns in migrations of Freshwater Cobbler, a totalof437weretaggedusingindividuallynumberedtbartagsateachmain channelsiteoverthestudyperiod(seeTable3).Thetotallengthofeachfish tagged and recaptured was measured to aid in the future validation of growth and movements of this species. Furthermore, in each month of the main migration period (late spring early autumn, see Figure 17), the gonadosomatic index (GSI) was calculated for both sexes. This index compares the proportion of the gonad to the overall body weight to determine spawning periods as a precipitous decline in the GSI is generally usedtoindicatetheperiodofpeakspawning.
24
RESULTSandDISCUSSION
Waterqualityinthemainchannelandtributaries
Climateduringthestudyperiod The analysis of the seasonal pattern in climate for the region revealed an atypical pattern in air temperature and rainfall for the sampling year(s) comparedwithhistoricaldata(Figures5and6).Specifically,thefirsthalfof thesamplingperiod (i.e.spring 2005and summer 20052006)wasunusually coolcomparedwiththelongtermaverage(Figure5).Furthermore,therewas an unusually late start to the wet season in 2006 (i.e. July compared with April/May historically) (Figure 6). Therefore, the seasonal patterns in fish movements described in this report may differ to that of a typical year and this interannual variation requires quantification by further seasonal sampling. For example, the relatively late onset of winter rains in 2006 probablyresultedindelayedseasonalsurfaceflowsinRosaBrook,Laymans BrookandMcAteeBrookthatarenotmaintainedbygroundwaterdischarge comparedtoMilyeannupBrookandPoisonGully,whichhaveperennialflow duetoYarragadeeAquiferdischarge.
32 30 28
Study period Long term (1887-2004)
Temperature (C)
26 24 22 20 18 16 14 Oct
2005
Nov
Dec
Jan
2006
Feb
Mar
Apr
May
Jun
Jul
Aug
Sep
Month
Figure5
Mean monthly maximum air temperature at Bridgetown during the study period and the long term mean (18872004, source: Australian Bureau of Meteorology). N.B. the considerably cooler spring 2005 and summer 2005 2006temperaturescomparedtothelongtermaverage.
25
Monthly rainfall during study Long term monthly rainfall (1887-2004)

180 160 140 120
Rainfall (mm)
100 80 60 40 20 0 Oct
2005
Nov
Dec
Jan
2006
Feb Mar
Apr
May
Jun
Jul
Aug
Sep
Month
Figure6
Monthly rainfall in Bridgetown during the study period compared with the longtermaverage(18872004,source:AustralianBureauofMeteorology).N.B theaboveaveragerainfallfromOctober2005January2006andconsiderably laterstarttothewinterrainfall(i.e.July2006)andverydryautumncompared withthelongtermaverage.
Aquaticenvironmentalvariables From the temperature data loggers (from which weekly means were determined to smooth the data), it was apparent that patterns of water temperatures in the Blackwood River and its tributaries corresponded with variationsinairtemperature(Figure7).However,theleastseasonalvariation (i.e. remained coolest in summer and warmest in winter), and thus more stable temperatures, were recorded in Milyeannup Brook. As noted, this system receives direct discharge from the Yarragadee Aquifer which maintains perennial flow for the lower ~2500m of stream length (see section on Milyeannup Brook) that probably results in the buffering of water temperaturescomparedwiththoseseasonallyflowingtributaries.Therewere no obvious differences between the weekly temperatures or temperatures duringmigrationsamplingtimesbetweensitesonthemainchannel(Figures 7and8).
26
Milyeannup Brook - Brockman Hwy Rosa Brook - Denny Rd McAtee Brook - Longbottom Rd Laymans Brook - Denny Rd Blackwood River- Milyeannup Pool Milyeannup Brook - Blackwood Rd Bridgetown mean maximum air temperature Blackwood River - Denny Rd
35
30
Water temperature (C)
25
20
15
10
5 Nov Jan Mar May Jul Sep
Month
Figure7 Mean weekly temperatures (1 SE) at the sampling sites in the tributaries, two main channel sites (Milyeannup Pool at the upstream point of Yarragadee discharge and Denny Rd receiving all of the Yarragadee discharge), and the maximumairtemperatureatBridgetown.N.B.thelowerseasonalfluctuationof the mean temperature in lower Milyeannup Brook (maintained by groundwater discharge) compared with those reliant on surface flows, and the marked influenceofairtemperatureonwatertemperatureatthesesites.
27
26 24 22
Denny Rd Milyeannup Pool Jalbarragup Quigup
Temperature (C)
20 18 16 14 12 10 Oct
2005
Nov
Dec
2006
Feb
Mar
Jun
Aug
Sep
Month
Figure8
Meantemperatures(1S.E.)atthesamplingsitesinthemainchannelofthe BlackwoodRiveroneachsamplingoccasion.
This consistency of water quality in the two perennial tributaries was highlighted by the relatively consistent conductivities recorded in these systems compared with systems that cease flowing. Those latter systems increase in conductivity during summer as a result of evapoconcentration (Figure 9a). The increased cumulative discharge of groundwater into the mainchannelduringsummerattheMilyeannupPoolandDennyRdresults inthosesiteshavingreducedconductivities(e.g.~2030S/cmatDennyRdin March) compared with sites upstream of the major zone of groundwater intrusion(e.g.~3550S/cmatJalbarragupinMarch)(Figures2and9b). The maintenance of relatively stable water quality variables (e.g. pH and oxygen,Figures1013)isknowntocreatestabilityinfaunalassociationsand maybefactorsresponsibleintheprovision ofrefugehabitatforrarespecies (Hattons & Evans 1998, Power et al. 1999, Murray et al. 2003, Humphreys 2006).
28
A
Rosa Brook Laymans Brook McAtee Brook Milyeannup Brook - upstream Milyeannup Brook - downstream St Johns Brook Poison Gully
1200
1000
Conductivity (S/cm)
800
600
400
200
0 Oct
2005
Nov
Dec
2006
Feb
Mar
Jun
Aug
Sep
Month
Denny Rd Milyeannup Pool Jalbaragup Quigup
8000
7000
Conductivity (S/cm)
6000
5000
4000
3000
2000
1000 Oct
2005
Nov
Dec
2006
Feb
Mar
Jun
Aug
Sep
Month
Figure9
A) Mean conductivities (1 S.E.) at the sampling sites in the tributaries at the times of sampling. N.B. the low seasonal fluctuation of the perennial lower MilyeannupBrookandPoisonGullycomparedwiththeotherseasonalsystems. B) Mean conductivities (1 S.E.) at the main channel sampling sites in the tributariesatthetimesofsampling.N.B.thelowsummerconductivitiesofthe sites receiving major groundwater discharge (i.e. Denny Rd and Milyeannup Pool)comparedwiththoseupstream(JalbarragupandQuigup)(seeFigure2).
29

Rosa Brook Laymans Brook McAtee Brook Milyeannup Brook - upstream Milyeannup Brook - downstream St John Poison Gully
7.5 7.0 6.5 6.0
pH
5.5 5.0 4.5 4.0 3.5 Oct

2005
Nov
Dec
2006
Feb
Mar
Jun
Aug
Sep
Month
Figure10 MeanpH(1S.E.)atthesamplingsitesinthetributaries.N.B.theincreased acidityinRosaBrookduringthedryperiodinMarchandJune2006.

Denny Rd Milyeannup Pool Jalbaragup Rd Quigup
8.5
8.0
7.5
pH
7.0
6.5
6.0
5.5 Oct
2005
Nov
Dec
2006
Feb
Mar
Jun
Aug
Sep
Month
Figure11 MeanpH(1S.E.)atthesamplingsitesinthemainchanneloftheBlackwood River.
30
18 16 14 12 10 8 6 4 2 Oct
2005
Rosa Brook Laymans Brook McAtee Brook Milyeannup Brook - upstream Milyeannup Brook - downstream St Johns Brook Poison Gully
Dissolved oxygen (ppm)
Nov
Dec
2006
Feb
Mar
Jun
Aug
Sep
Month
Figure12
Meandissolvedoxygen(1S.E.)atthesamplingsitesinthetributariesofthe BlackwoodRiveratthetimesofsampling.N.B.thelessseasonalfluctuation in lower Milyeannup Brook compared with tributaries not receiving YarragadeeAquifergroundwater.
Denny Rd Milyeannup Pool Jalbarragup Quigup
20 18 16 14 12 10 8 6 4 Oct
2005
Dissolved oxygen (ppm)
Nov
Dec
2006
Feb
Mar
Jun
Aug
Sep
Month
Figure13
Meandissolvedoxygen(1S.E.)atthesamplingsitesinthemainchannel of the Blackwood River. N.B. the greater minimum level of dissolved oxygen at the Denny Rd site that receives all of the Yarragadee Aquifer dischargeinthedryperiod(March).
31
Rosa Brook had the greatest discharge of any tributary; peaking in October 2005, at the start of the study (Figure 14). Milyeannup Brook and Poison Gully (although not gauged) continued to flow throughout the dry months due to groundwater discharge (Figure 14). There was a general increase in thedischargeratesmovingdownstreaminthemainchannelsites(Figures2 and15).Asmentioned,climaticallythiswasanatypicalyearasreflectedby relativelylowdischargeupuntilAugust2006(Figure15).Ofparticularnote isthegreaterdischargeatGingilupcomparedwithDarradupduringthedry months (FebruaryJuly, Figure 2). This is due to Gingilup receiving the majorityoftheYarragadeeAquiferdischargeintothemainchannelwhereas Darradup is upstream from the discharge zone (Figure 15). This highlights thefactthatgroundwatercontributestobetween30and100%ofthesummer dischargeoftheBlackwoodRiver(Strategen2006).
4
Rosa Brook Laymans Brook McAtee Brook Milyeannup Brook - upstream Milyeannup Brook - downstream Poison Gully
Mean discharge (m 3/sec)
0 Oct
2005
Nov
Dec
2006
Feb
Mar
Jun
Aug
Sep
Month
Figure14 Mean discharge ( 1 SE) at the sampling sites in the tributaries of the BlackwoodRiveratthetimesofsampling.N.B.thecontinuancyofdischarge inlowerMilyeannupBrookcomparedtotheseasonaltributaries.
32
35
30
Nannup Darradup Gingilup Hut pool
25
Discharge (m 3/sec
20
15
10
0
ct 0 No 5 v 0 De 5 c 0 Ja 5 n 0 Fe 6 b 0 M 6 ar 0 Ap 6 r0 M 6 ay 0 Ju 6 n 06 Ju l0 Au 6 g 0 Se 6 p 0 O 6 ct 0 No 6 v 0 De 6 c 06
Month
Figure15
Monthlymeandischarges(1SE)inmainchannelsitesoftheBlackwoodRiver at the times of sampling. N.B. the greater discharge in Gingilup (receiving downstream of groundwater discharge zones) compared with Darradup (upstream of the Yarragadee discharge zone) from February June 2006 (see alsoFigure2).
Themaintenanceofrelativelylowmainchannelsalinitiesasaconsequenceof groundwater intrusions has considerable ecological implications as during summer, when the majority of tributaries cease flowing, many fish must retreatintothemainchannel.Duringwinter,whenthehighestconductivities areexperienced(Figure9),thoseindividualscanutilisethethenflowingfresh tributariestoescapetheelevatedmainchannelsalinitiesthatmayexceedtheir tolerance levels. Therefore, saltintolerant species, particularly Balstons PygmyPerch,WesternPygmyPerchandNightfish,thatarecurrentlyableto utilise this diluted section ofthe BlackwoodRiver,maynotbeabletodoso should a reduction in freshwater input in summer occur to a degree that salinityincreasestoalevelthatexceedstheirsalinitytolerances.
33
Speciescapturesummary
During this study, six endemic freshwater fish species, three estuarine fish species and three introduced fish species were captured. The anadromous (i.e. migrates into rivers from the ocean to breed) Pouched Lamprey, a southern hemisphere agnathan (i.e. jawless fish) was also captured, but was foundinonlytwotributaries.Thesixfishspeciescapturedthatareendemic to southwestern Australia were the Freshwater Cobbler, Western Minnow, Mud Minnow, Balstons Pygmy Perch, Western Pygmy Perch, and the Nightfish. The estuarine species captured were the Western Hardyhead, Southwestern Gobyandthe SwanRiverGoby.Thethreeintroducedfishes capturedweretheEasternMosquitofish,GoldfishandRainbowTrout. Four species of endemic freshwater crayfish were captured, including the Marron,Gilgie,RestrictedGilgieandKoonac. Below is an account of the distribution, population demographics and migration patterns of each species. See also Section 2 for information regardingcrayfishburrowingactivity.
FreshwaterCobbler:ThelargestnativefreshwaterfishinthesouthwestofW.A.
34
Table1
Thetotal(andadjusted)numberofeachspeciesoffishandfreshwater crayfishcapturedinfykenetsintheBlackwoodRivermainchannelsites.
SPECIES Total number (adjusted for stream width) of individuals caught in the Blackwood main channel using Fyke nets. MOVEMENT Downstream Endemic freshwater fishes
Freshwater Cobbler Western Minnow Mud Minnow Balstons Pygmy Perch Western Pygmy Perch Nightfish 526 (1539.3) 22 (175) 0 0 14 (54) 11 (73) 1280 (5729.5) 463 (3193.3) 0 2 (40) 0 4 (28.3) 1806 (7268.8) 485 (3368.3) 0 2 (40) 14 (54) 15 (101.3)
Upstream
Total # Captured
Estuarine fishes
South-west Goby Swan River Goby Western Hardyhead 94 (563) 6 (34.7) 13 (59.7) 26 (158.3) 4 (10) 12 (69.7) 120 (721.3) 10 (44.7) 25 (129.3)
Introduced fishes
Eastern Mosquitofish Goldfish Rainbow Trout 14 (75) 0 0 13 (45) 0 0 27 (120) 0 0
Endemic crayfishes
Smooth Marron Gilgie Restricted Gilgie Koonac 18 (100) 4 (22.3) 0 0 11 (70.5) 3 (31.7) 0 0 29 (170.5) 7 (54) 0 0
Total number
1624 (6591)
1908 (9808)
3532 (16399)
35
FreshwaterCobbler
Habitatassociations The Freshwater Cobbler is essentially restricted to the main channel of the Blackwood River (Figure 16, Appendices 1 and 2). The few individuals capturedinthetributariesweregenerallysmallerfishwithonlyfive,twoand 17 captured in Rosa Brook, McAtee Brook and Milyeannup Brook, respectively (Figure 17). This was expected given this relatively large (comparedtoothernativespeciesoftheregion)fishismorecommonlyfound inthelargerriversandreservoirsinthisregion. Migrationpatterns On almostallsamplingoccasions, thestrength of theupstream migrationof FreshwaterCobblerwasgreaterthanthedownstreammigration(Figure16). The migration strength peaked in late spring and summer, with greatest migrationstrengthbeingrecordedinthemoredownstreamsitesthatreceived greater groundwater discharge (i.e. Denny Rd and Milyeannup Pool) compared to the upstream sites (i.e. Jalbarragup and Quigup). Spatial differences in migratory patterns existed within the main channel with the peak upstream migrations in the downstream sites occurring during February, compared to March and November in Quigup and Jalbarragup, respectively(Figure16).MovementofFreshwaterCobblerwasataminimum duringwinter. Furthermore, the spawning period of female Freshwater Cobbler coincided with their major migration period between late spring and summer as indicatedbyadeclineintheirGSIduringthattime(indicatingthateggshad beenreleasedfromovaries)(Figure18). ThestrengthofboththeupstreamanddownstreammigrationsofFreshwater CobblerinthemainchanneloftheBlackwoodRiverovertheentiresampling periodatallsiteswaspositivelycorrelatedwithwatertemperature(Table2). Watertemperaturewasfoundtoaccountfor~53%(p=0.00)ofupstreamand ~34%(p=0.003)ofdownstreammovement(Figures19and20).Thisreflected
36
the fact that Freshwater Cobbler movements increased during periods of elevatedwatertemperatures(i.e.summer). ThemeanstrengthofupstreammovementofFreshwaterCobbleratthemain channel sites during the peak movement period (i.e. late spring to autumn: November to July samples inclusive) was highly correlated with the mean discharge at those sites over that period (Figure 21). Regression analysis revealed that the overall mean monthly discharge between November and July at these sites explained ~96% (p=0.014) of the variation between main channelsitesinFreshwaterCobblermovementintheBlackwoodRiver.That is,thegreaterthesummerdischargeatthesesites,thegreaterthestrengthof migration of this species. This movement is probably due to this species accessinghabitatsforspawningandfeeding. Ofthe437taggedFreshwaterCobbler,atotalof86(19.7%)were recaptured (Table3).Ofthese,68wererecapturedonce,12twice,fourthreetimesand twowererecapturedfourtimes(Table3).Withtheexceptionofonefish,all were caught at the initial tagcapture site. This suggests that there is a relativelyhighdegreeofsitefidelitybythisspeciesintheBlackwoodRiver. Although a high degree of site fidelity occurs in this system, there are nonethelesslargelocalisedupstreammigrationsbythisspeciesduringtimes oflowflowasaprecursortospawning.Asmuchofthedryperioddischarge intheBlackwoodRiverisadirectresultofgroundwaterdischarge(30100% in the driest two months), this species appears reliant on this groundwater discharge to facilitate such spawning migrations. This groundwater dischargeisthereforeimportantinprovidingadequatepassagethroughriffle zones that would otherwise be barriers to its migration; and would be particularimportantinyearsoflowinputofsurfaceflows.
37

Freshwater Cobbler (T. bostocki)
Downstream movement Upstream movement
1400
Denny Road
Mean number of fish
1200 1000 800 600 400 200 0
1400
Milyeannup Pool
Mean number of fish
1200 1000 800 600 400 200 0
NS
NS
1400
Jalbarragup
Mean number of fish
1200 1000 800 600 400 200 0
1400
Mean number of fish
1200 1000 800 600 400 200 0
Quigup
NS
ry er er er ch tob emb emb brua Mar v c Oc Fe No De Ju ne g Au
NS
t r us mbe p te Se
Figure16
Upstream and downstream movement of Freshwater Cobbler at the four mainchannelsites.NS=notsampled.
38

Freshwater Cobbler (T. bostocki)
10
Rosa Brook
Mean number of fish
NF NF
10
Layman Brook
Mean number of fish
DRY DRY
10
Milyeannup Brook
Mean number of fish Mean number of fish
8
10
McAtee Brook
6
NF
ry er er er ch tob emb emb brua Mar v c Oc Fe No De
NF
st er ne Ju Augu temb p Se
Month
Figure17 Upstream and downstream movement of Freshwater Cobbler in the four tributaries.
39
Mean Gonadosomatic Indices (+1SE)

5 19 4 Female Male
Gonadosomatic index
37 2
47 1 65 0 3 22 11 February 20
November
December
March
Month

Figure18 Meangonadosomaticindices(GSI)(+1SE)formaleandfemaleFreshwater CobblerinthemainchanneloftheBlackwoodRiverbetweenlatespringand earlyautumn.
40

3.5 log10N = 4.77*log10T - 3.86 r2 = 0.54
3.0
log10 mean frequency of fish
2.5
2.0
1.5
1.0
0.5 1.0 1.1 1.2 1.3

o
1.4
log10 mean temperature ( C)
Figure19RelationshipbetweenthemeanstrengthoftheupstreammigrationofFreshwater Cobbler and the mean temperature in the Blackwood River main channel throughoutthesamplingperiod.N.B.datawerelog10transformedandmigration numberwasstandardisedforeffort,seetextfordetails.
log10N = 3.53*log10D - 3.22 r2 = 0.37 2.5
2.0
1.5
1.0
0.5
0.0 1.0 1.1 1.2 1.3

o
1.4
log10 mean temperature ( C)
Figure20 RelationshipbetweenthemeanstrengthofdownstreammigrationofFreshwater Cobbler and the mean temperature in the Blackwood River main channel throughoutthesamplingperiod.N.B.datawerelog10transformedandmigration numberwasstandardisedforeffort,seetextfordetails.
41

2.8 log10N = 2.63*log10D +2.11 r2 = 0.97
2.6
2.4
2.2
2.0
1.8 -0.05 0.00 0.05 0.10 0.15

3
0.20
0.25
log10 mean discharge (M /sec)
Figure21
Relationship between the mean strength of the upstream migration of Freshwater Cobbler and the mean discharge in the Blackwood River main channelbetweenNovemberandJuly.N.B.Datawerelog10transformedand migrationnumberwasstandardisedforeffort,seetextfordetails.
42
Table2 CorrelationsbetweenoverallmeanupstreamanddownstreammovementsofFreshwaterCobberinthe mainchannelsitesoftheBlackwoodRiverandprevailingenvironmentalvariablesduringthemigration period(NovembertoJuly).N.B.Datawerelog10transformed,*denotescorrelationissignificantatthe 0.05level(2tailed).

Log temperature .358 .642 .733 .267 -.498 .502 -.470 .530 -.426 .574 .273 .727 Log conductivity Log discharge Upstream movement
Log pH
Log O2
Log conductivity
Pearson Correlation Sig. (2-tailed) Pearson Correlation Sig. (2-tailed) Pearson Correlation Sig. (2-tailed) Pearson Correlation Sig. (2-tailed) Pearson Correlation Sig. (2-tailed) Pearson Correlation Sig. (2-tailed)
Log pH
.414 .586 -.983* .017 -.787 .213 -.680 .320 -.690 .310 -.444 .556 -.837 .163 -.871 .129 -.241 .759 .752 .248 .634 .366 .550 .450 .986* .014 .700 .300 .687 .313
Log O2
Log discharge
Upstream movement
Downstream movement
43
Table3
FreshwaterCobblertaggedandrecapturedinmainchannelsitesoftheBlackwoodRiver.N.B.Includes%recapturedper siteand%totalofallrecaptureswhencomparedtototalnumbertagged.
SITE Number Tagged 215 42 110 70 437 # Recaptured (%) 42 (19.5) 7 (16.7) 17 (15.5) 2 (2.9) 68 (15.6) 12 (2.7) 4 (0.9) 2 (0.5) 4 (3.6) 3 (2.7) 2 (1.8) # Recaptured Twice (%) 8 (3.7) # Recaptured 3 times (%) 1 (0.5) #Recaptured 4 Times (%)
Denny Road Milyeannup Pool Jalbarragup Quigup TOTAL (%)
44
WesternMinnow
Habitatassociations TheWesternMinnowwascapturedatthemajorityofsitessampledonmost occasions, with large numbers recorded in both the main channel sites (Appendix 1) and in the tributaries (Appendix 2). This widespread distribution,beingpresentinnearlyallhabitatssampled,reflectsthisspecies tolerance to a wide range of salinities; having previously been recorded in salinities up to ~24 ppt or ~two thirds the salinity of seawater (Morgan and Beatty2004). Migrationpatterns TherewerelimitedmovementsofWesternMinnowinthetwomostupstream main channel sites compared to the more downstream sites, i.e. Denny Rd and Milyeannup Pool (Figure 22). Within these latter sites, the upstream movement of Western Minnow was strongest during winter and peaked in Augustwith,onaverage,over300individualsrecordedmovingupstreamper day.Thesefishwerelargeadultsthatwerelikelytobemovingasaprecursor to spawning (Figures 2325). Migration into Milyeannup Brook was high in Augustandtherewaslimitedmovementofadultsintotheothertributariesat this time. Later migration of adults was recorded into the other tributaries fromAugusttoNovember.UpstreammigrationsofadultWesternMinnow continued in Milyeannup Brook throughout the entire sampling period; presumably as a consequence of the perennial flows of the system resulting fromYarragadeeAquiferdischarge(Figures14and26). The marked contrast in population demographics of Western Minnow in MilyeannupBrookcomparedtotheothertributariesisfurtherhighlightedby the considerable number of new recruits (i.e. offspring) recorded in Milyeannup Brook two months earlier than other systems; strongly suggesting that spawning activity was earlier in this system (Figures 27 and 28).Forexample,manyofthesenewrecruitsmigrateddownstreamintothe main channel during October to December in Milyeannup Brook, compared
45
to December for Rosa Brook and McAtee Brook. Only limited recruitment occurredinLaymanBrook. TheearlierrecruitmentoffishfromMilyeannupBrookisfurtherhighlighted bythelargersizeofthiscohortcomparedtothoseinRosaBrookinDecember (i.e.modallength5055mmTLcomparedto2530mmTL)(Figure27).This earlier spawning in Milyeannup Brook, presumably as a consequence of perennialflowsallowingearlieraccesstothetributary,isfurtherhighlighted whenconsideringthatthenewrecruitsinthisstreamhadamodallengthof 3540mmTLduringOctober,whichis10mmgreaterthanthenewrecruitsin RosaBrooktwomonthslater(Figure27). Examination of lengthfrequency histograms of fish caught in main channel sites compared to tributary sites reveals that the vast majority of Western Minnows that we captured that were less than 40 mm TL were only found withinthetributaries.Thisstronglysuggeststhatbreedingtakesplacewithin tributariesand that these habitats are therefore vital spawning areas for this species. TherearesubstantialdifferencesinthepopulationdemographicsofWestern Minnows in the main channel sites. Specifically, fish captured in the two most downstream sites grew to a substantially larger size implying that the species had greater longevity at the downstream sites compared to the two upstream sites. For example, of the fish that were greater than 100 mm TL, almostallwerefoundattheDennyRdandMilyeannupPoolsites(thatboth receiveYarragadeeAquiferdischarge). The upstream and downstream migration of the Western Minnow in the varioustributarieswerebothfoundtobepositivelycorrelatedwiththemean discharge from the tributaries during the major flow period (August to December)(Table4).Fromtheregressionanalysis,meandischargeexplained ~92% (p=0.027) and 87% (p=0.044) of the variation in the mean downstream and upstream migration of Western Minnow between the tributaries during this period (Figures 29 and 30). This suggests that the larger the discharge from tributaries during peak flow periods, the greater the usage of those streams by the Western Minnow, presumably for spawning. However, the perennial flows of Milyeannup Brook would provide earlier access to spawningsitesregardlessofsurfacerunoff(i.e.rainfall).
46

Western Minnow (G. occidentalis)
500
Denny Road
Mean number of fish
400
300
200
100
700
Milyeannup Pool
Mean number of fish
600 500 400 300 200 100 0
NS NS
500
Jalbarragup
Mean number of fish
400
300
200
100
500
Quigup
Mean number of fish
400
300
200
100
NS NS
Oc tob emb emb bru v c Fe No De er er er a ry Ma rc h Ju ne Au r st g u em b e pt Se
Month
Figure22
UpstreamanddownstreammovementofWesternMinnowatthefourmain channelsites.NS=notsampled.
47

Western Minnow (Galaxias occidentalis)
20 15 10 5 0 20 15 10 5 0 20 15 10 5 0 Downstream Migration Upstream Migration
2005 October
n=37
November
n=2
December
n=4
Number of Fish
20 15 10 5 0 20 15 10 5 0 60 50 40 30 20 10 0
2006 February
n=6
March
n=17
June
n=163
40 30 20 10 0
August
n= 177
20 15 10 5 0
0 10 20 30 40 50 60 70 80 90 00 10 20 30 40 50 60 1 1 1 1 1 1 1
September
n=37
Total Length(mm)
Figure23
CombinedlengthfrequencyhistogramsofWesternMinnowscapturedusing fykenetsinthefourmainchannelsites.
48

20 15 10 5 0 20 15 10 5 0 20 15 10 5 0 20
Denny Rd
2005 October
60 50 40 30 20 10 0 60 50 40 30 20 10 0 60 50 40 30 20 10 0 60 50 40 30 20 10 0 60 50 40 30 20 10 0 60 50 40 30 20 10 0 60 50 40 30 20 10 0 60 50 40 30 20 10 0
Milyeannup Pool
2005 October
NS November
November
NS December
December
Number of fish
10 5 0 20 15 10 5 0 20 15 10 5 0 20 15 10 5 0 20 15 10 5 0
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0 17 0 18 0
March
Number of fish
15
2006 February
2006 February
March
June/July
June/July
August
August
September
September
Total length (mm)
Figure24
LengthfrequencyhistogramsofWesternMinnowscapturedusingseinenets and electrofishing in the two downstream main channel sites. NS = not sampled.
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0 17 0 18 0
Total length (mm)
49

Jalbarragup
2005 October
20 15 10 5 0 20 15 10 5 0 20 15 10 5 0 20
20 15 10 5 0
Quigup
2005 October
November
20 15 10 5 0 20 15 10 5 0 20
November
December
December
Number of fish
10 5 0 20 15 10 5 0 20 15 10 5 0 20 15 10 5 0 20 15 10 5 0
Number of fish
15
2006 February
15 10 5 0 20 15 10 5 0
2006 February
March
March
June/July
20 15 10 5 0
June/July
August
20 15 10 5 0
August
NS September
September
20 15 10 5 0
NS
0 10 20 30 40 50 60 70 80 9 100 110 120 130 140 150 160 170 180 0
Total length (mm)
0 10 20 30 40 50 60 70 80 9 100 110 120 130 140 150 160 170 180 0
Total length (mm)
Figure25 LengthfrequencyhistogramsofWesternMinnowscapturedusingseinenets and electrofishing in the two upstream main channel sites. NS = not sampled.
50
Western Minnow (G. occidentalis)

250
Rosa Brook
Mean number of fish
200
150
100
50
NF NF
250
Layman Brook
Mean number of fish
200
150
100
50
DRY DRY
250
Milyeannup Brook
Mean number of fish
200
150
100
50
250
McAtee Brook
Mean number of fish
200
150
100
50
NF
NF
Ju ne g Au t r us mbe pte Se
Month
Figure26
Upstream and downstream movement of Western Minnows in the four tributariessampled.NF=notflowingandthuslimitedconnectivitybetween pools.
51
Rosa Brook
50 40 30 20 10 0 50 40 30 20 10 0 120 100 80 60 40 20 0
Western Minnow (Galaxias occidentalis) Milyeannup Brook

Downstream Upstream 140 120 100 80 60 40 20 0 100 Downstream Upstream
2005 October
n=16
2005 October
n=339
November
n=53
80 60 40 20 0
November
n=306
December
n=310
50 40 30 20 10 0
December
n=117
Number of Fish
50 40 30 20 10 0 50 40 30 20 10 0 50 40 30 20 10 0
Number of Fish
2006 February NOT FLOWING
50 40 30 20 10 0 50 40 30
2006 February
n=34
March
March
n=13
NOT FLOWING
20 10 0
June
n=17
100 80 60 40 20 0
June
n=241
50 40 30 20 10 0
August
n=46
50 40 30 20 10 0
August
n=162
50 40 30 20 10 0
0 10 20 30 40 50 60 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0 70
September
n=96
50 40 30 20 10 0
0 10 20 30 40 50 60 70 80 90 00 10 20 30 40 50 60 1 1 1 1 1 1 1
September
n=169
Total Length (mm)
Total Length (mm)
Figure27
LengthfrequencydistributionsofWesternMinnowscapturedinRosaBrookand MilyeannupBrookseparatedbydownstreamandupstreammovement.N.B.the earlier recruitment of small fish (offspring) into the Milyeannup Brook population (October versus December) and the earlier upstream migration of prespawningadultsinMilyeannupBrook(JuneversusDecember).
52
Western Minnow (Galaxias occidentalis)

40 30 20 10 n=60 0 40 30 20 10 0 40 30 20 10 0
Layman Brook
Downstream Upstream
40 30
McAtee Brook
Downstream Upstream
2005 October
20 10
2005 October
n=58
0 40 30
November
n=25
20 10 0 40
November
n=68
December
n=0
30 20 10 0
December
n=37
Number of Fish
40 30 20 10 0
Number of Fish
40 30 20 10 0 40
2006 February DRY
40 30 20 10 0 40 30 20 10 0
March DRY
30 20 10 0 40
March NOT FLOWING
June
30 20
June
n=10
DRY
10 0
40 30 20 10 0
40
August
n=22
30 20 10 0
August
n=113
40
September
30 20 10 0
10 20 30 0 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0
40 30 20 10 0
10 20 30 50 60 70 0 40 80
September
n=149
n=49
Total Length (mm)
Total Length (mm)
Figure28
LengthfrequencydistributionsoftheWesternMinnowcapturedinLayman Brook and McAtee Brook separated by downstream and upstream movement.
90 10 0 11 0 12 0 13 0 14 0 15 0 16 0
53

1.3 log10N = 0.39*log10D + 1.19 r2 = 0.91
1.2
1.1
1.0
0.9
0.8
0.7
0.6 -1.4 -1.2 -1.0 -0.8 -0.6

3
-0.4
-0.2
0.0
Figure29
Relationship between the mean strength of upstream migration of Western Minnows within the major flow period (August and December) and the mean discharge in the four tributaries during that period. N.B. Data were log10 transformed and migration was standardised for effort, see text for details.
2.0 log10N = 0.74*log10D + 1.89 r2 = 0.95
1.8
1.6
1.4
1.2
1.0
0.8
0.6 -1.4 -1.2 -1.0 -0.8 -0.6

3
-0.4
-0.2
0.0
Figure30
Relationship between the mean strength of downstream migration of Western Minnows within the major flow period (August to December) and themeandischargeinthefourtributariesduringthatperiod.N.B.Datawere log10 transformed and migration was standardised for effort, see text for details.
54

Table4 CorrelationsbetweenupstreamanddownstreammovementofWesternMinnowsinthetributariesoftheBlackwoodRiverandprevailing environmentalvariablesduringthemigrationperiod.N.B.Datawerelog10transformed,*denotescorrelationissignificantatthe0.05level (2tailed).
Log conductivity
Log temperature .686 .314 -.508 .492 .229 .771 -.131 .869 -.129 .871 .025 .975
Log conductivity
Log pH
Log O2
Log discharge
Upstream movement
Log pH
-.677 .323 .589 .411 .600 .400 .633 .367 .666 .334 .182 .818 -.573 .427 -.379 .621 -.747 .253 .311 .689 .563 .437 .187 .813 .956* .044 .973* .027 .879 .121
Log O2
Log discharge
Upstream movement
Downstream movement
55
MudMinnow
Habitatassociations The Mud Minnow was only captured in the tributaries of the Blackwood River(Appendix2)andthereforeisolationofthepopulationsinthesesystems maybeoccurringwiththemainchanneleffectivelyactingasasaltbarrierto population mixing; however, this requires further investigation. It was recordedinPoisonGully,MilyeannupBrook,RosaBrookandMcAteeBrook; however,notinLaymansBrook(Appendix2).Thissuggeststhatthisspecies prefers tributaries with either permanent (Milyeannup Brook and Psoin Gully)orextended(RosaBrookandMcAteeBrook;thatbothhavesubstantial remnant pools when they cease to flow) flow periods. Mud Minnows naturally exist in lowabundancescomparedtoother nativespecies(such as the Western Minnow) as was the case in this study with the species being recordedinlowernumbersthananyothernativefreshwaterfish;andonly90 individualsbeingcaptured.Morgan&Beatty(2005)alsoreportedthisspecies in St John Brook and Red Gully. The upper reaches of Rosa Brook, which receive Leederville Aquifer discharge, are a known refuge for the species in thatsystem(Morganetal.2004a). Migrationpatterns Due to the relatively low numbers of Mud Minnows, there were few clear obvious trends in the movement patterns of this species in these systems (Figure31).Thelargest numbers recordedinfykenetswereinMilyeannup Brookwhere,onaverage,~12andsixfishwererecordedmovingdownstream perdayinOctoberandNovember,respectively(Figure32).Thesefishwere small fish that had recently metamorphosed suggesting that upstream habitats of Milyeannup Brook was utilised for spawning and that a downstream migration of recruits was occurring. This species is known to have a one year lifecycle (Pen et al. 1991) and in the case of Rosa Brook, the breedingperiodisbetweenAugustandOctober(Morganetal.2004).
56

Mud Minnow (G. munda)
20
RosaBrook
Mean number of fish
15
10
NF NF
20
Layman Brook
Mean number of fish
15
10
30
Milyeannup Brook
Mean number of fish
25 20 15 10 5 0
20
Mean number of fish
McAtee Brook
15
10
NF NF
ry ch tob emb emb brua Mar v c Oc Fe No De er er er Ju ne g Au t r us mbe te ep S
Month
Figure31
Upstream and downstream movement of Mud Minnow in the four tributariessampled.NF=notflowingandthuslimitedconnectivitybetween pools.
57
Mud minnow (Galaxiella munda)

10 8 6 4 2 0 10 8 6 4 2 0 10 8 6 4 2 0
Rosa Brook
Downstream Upstream
10 8 6 4 2 0 10
Milyeannup Brook
Downstream Upstream
2005 October
n=0
2005 October
n=15
November
n=0
8 6 4 2 0
November
n=18
December
n=2
10 8 6 4 2 0
December
n=0
Number of Fish
10 8 6 4 2 0 10 8 6 4 2 0 10 8 6 4 2 0
Number of Fish
10 8 6 4 2 0 10 8 6
2006 February
n=3
March
March
n=10
NOT FLOWING
4 2 0
June
10 8 6 4 2 0
June
n=0
n=2
10 8 6 4 2 0
August
n=2
10 8 6 4 2 0
August
n=1
10 8 6 4 2 0 Total Length (mm)

80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0 10 20 30 50 60 70 40 0
September
n=0
10 8 6 4 2 0
0 10 20 30 40 50 60 70 80 90 00 10 20 30 40 50 60 1 1 1 1 1 1 1
September
n=0
Total Length (mm)
Figure32 LengthfrequencydistributionsofMudMinnowcapturedinRosaBrookand MilyeannupBrookseparatedondownstreamandupstreammovement.
58
BalstonsPygmyPerch
Habitatassociations Balstons Pygmy Perch is the most restricted fish species found within the BlackwoodRivercatchmentandhasrecently(2006)beenlistedasVulnerable undertheEPBCActandlistedbyCALMasSchedule1(WildlifeConservation Act, 1950). Balstons Pygmy Perch was effectively only captured within Milyeannup Brook with 3160 of the 3177 fish (or 99.46%) being recorded in this stream; many of these juveniles with the base population found to be much less much less (see section Milyeannup Brook Case Study) (Figure 33, Appendix 2). Thus, Milyeannup Brook is the crucial refuge habitat for this speciesintheBlackwoodRivercatchment;probablyduetotheconsistencyof suitable available habitat facilitated by the permanency of flow due to groundwaterdischargeinthissystem. FourindividualswerecapturedinMcAteeBrookduringAugust2006;whilea further 13 fish were captured in Milyeannup Pool near the mouth of Milyeannup Brook. The lengths recorded for this species in Milyeannup Brook were considerably greater than has previously been reported for the species (see Morgan et al. 1995). The lengthfrequency distribution of this species suggest that the modal length of the fish captured in August (5070 mmTL)arelikelytobe1yearold;whilethosefishgreaterthan70mmTLare most likely at the end of their second or third year of life (Figure 34). The relativelyhighlongevityoftheMilyeannupBrookpopulationcontrastswith thoseelsewherethathaveonlybeenfoundtoliveforjustoveroneyear(see Morganetal.1995). Migrationpatterns ThemajorupstreammigrationofadultBalstonsPygmyPerchinMilyeannup Brook occurred during winter (i.e. August) with considerable downstream movement of presumably spent (recently spawned) adults in August and September and downstream migration of juveniles occurring in November and December (Figure 33). The upstream migration period in Milyeannup Brookcoincidedwith theknownspawningperiodof thespecies(Morganet al.1995)withthelengthsrecordedherebeing~5095mmTL;i.e.adultsfish.
59
Thus,thisupstreammigrationwasundoubtedlyadultsreadytospawn;likely moving upstream to offset the downstream movement of eggs and/or larvae/juveniles. During September there was a considerable downstream movement of spent (recently spawned) fish; suggesting the peak spawning period was August in Milyeannup Brook. Subsequently, large numbers of new recruits were captured moving downstream in November and December. During December a few individuals were captured near the mouth of MilyeannupBrook(inthemainchannel)anditisevidentthatthesefishhad leftthestream.However,anumberalsomovedbackintothestreamatthis time. During August, a small number of adults were also captured moving upstreaminMilyeannupPool,presumablyontheirwaytoMilyeannupBrook tocommencespawning(Figure35).
Balston's Pygmy Perch (N. balstoni)

800
Rosa Brook
Mean number of fish
600
400
200
NF NF
20
Layman Brook
Mean number of fish
15
10
800 700
Milyeannup Brook
Mean number of fish
600 500 200 150 100 50 0
100
McAtee Brook
Mean number of fish
80
60
40
20
NF NF
0
ry er er er ch tob emb emb brua Mar c v Oc Fe No De
Month
Figure33
UpstreamanddownstreammovementofBalstonsPygmyPerchinthefour tributariessampled.
60

Balston's Pgymy Perch (N. balstoni)
20 15 10 5 0 120 80 40 0 60 40 20 0
Milyeannup Brook
Downstream Upstream
2005 October
November
December
Number of Fish
20 15 10 5 0 20 15 10 5 0 20 15 10 5 0 40 30 20 10 0 20 15 10 5 0
0 10 20 30 40 50 60 70 80 90 00 10 20 30 40 50 60 1 1 1 1 1 1 1
2006 February
March
June
August
September
Total Length (mm)
Figure34 LengthfrequencydistributionsofBalstonsPygmyPerchcapturedinMilyeannup Brook separated on downstream and upstream movement. N.B. adults moving upstreamtospawninAugust,spentadultsmovingdownstreaminSeptember,and newrecruitsmovingdownstreaminNovemberandDecember.
61
Baltston's Pgymy Perch (N. balstoni)

100
Denny Road
Mean number of fish
80
60
40
20
100
Milyeannup Pool
Mean number of fish
80
60
40
20
NS NS
100
Jalbarragup
Mean number of fish
80
60
40
20
100
Quigup
Mean number of fish
80
60
40
20
NS NS
to Oc r r r be mbe mbe ruary arch M b ve ce Fe No De Ju ne st er gu emb Au pt Se
Month
Figure35
UpstreamanddownstreammovementofBalstonsPygmyPerchinthefour mainchannelsitessampled.
62
WesternPygmyPerch
Habitatassociations WesternPygmyPerchwererecordedmovingateachsitewithinRosaBrook, MilyeannupBrookandMcAteeBrookoneachsamplingoccasion(Figure36). This species was not captured in Layman Brook and very few were found moving in the main channel sites; with none found migrating at the most upstreamsite,Quigup(Figure37).Veryfewindividualswerecapturedinthe main channel sites during the quantitative sampling (Appendix 1). This suggeststhatthisspeciesislargelyreliantonthefreshwatertributariesinthis region;reflectingarelativelylowtolerancetosalineconditions. Migrationpatterns Both upstream and downstream movements of Western Pygmy Perch were recorded at most tributary sites on most sampling occasions (Figure 36). Migration strength was greatest within Rosa Brook; which appeared to support the largest population of Western Pygmy Perch of any system. As thisspeciesisknowntobreedinspring,itislikelythatmuchoftheupstream migration impetus were for reproductive purposes. The subsequent downstreammovementbythisspeciesinRosaBrookinDecember,aswellas inMilyeannupBrookandMcAteeBrook,appearedtoconsistoffishthathad spawned(i.e.spent)andwereleavingthesystemasflowsubsidedwithsome newrecruitsalsobeingrecordedinMilyeannupBrook.However,withinthe perennial Milyeannup Brook, there continued to be upstream and downstreammigrationsthroughoutsummerandearlyautumn;facilitatedby the continuation of flows in this system resulting from direct groundwater discharge(Figure36). WesternPygmyPerchareoftenabundantinthemainchannelofotherriver systems in southwestern Australia and the low and sporadic catches of the specieswithinthemainchannelsitesoftheBlackwoodRivermaybedueto unsuitable water quality (i.e. salinised) for the species at these sites (Figures 37,40).
63
The upstream movement of the Western Pygmy Perch in tributaries was positively correlated with mean dissolved oxygen levels during the flow period in the tributaries (although at a significance level of p<0.1) (Table 5). Meandissolvedoxygenlevelswerefoundtoaccountfor~96%(p=0.088)ofthe variation between the tributaries in the upstream movement of Western Pygmy Perch (Figure 41). This relationship suggests that Western Pygmy Perch may prefer more highly oxygenated streams for spawning, although undoubtedly other habitat parameters not analysed here would also be of importance (such as degree of instream vegetation for egg deposition and attachment).
Western Pygmy Perch (E. vittata)

80
Rosa Brook
Mean number of fish
60
40
20
NF NF
80
Layman Brook
Mean number of fish
60
40
20
40
Milyeannup Brook
Mean number of fish Mean number of fish
30
20
10
80
60
McAtee Brook
40
20
NF NF
ry er er er ch tob emb emb brua Mar v c Oc Fe No De st er ne Ju Augu temb p Se
Month
Figure36
Upstream and downstream movement of Western Pygmy Perch in the four tributaries.
64

Western Pygmy Perch (E.vittata)
20
Denny Road
Mean number of fish
15
10
20
Milyeannup Pool
Mean number of fish
15
10
NS NS
40
Jalbarragup
Mean number of fish
30
20
10
40
Quigup
Mean number of fish
30
20
10
NS NS
ry er er ch mb emb brua Mar to ve c Oc Fe No De r be Ju ne g Au t r us mbe te ep S
Month
Figure37
Upstream and downstream movement of Western Pygmy Perch in the four mainchannelsites.
65

Western Pygmy Perch (Edelia vittata)
10
Rosa Brook
Downstream Migration Upstream Migration
10
Milyeannup Brook
Downstream Migration Upstream Migration
2005 October
n=19
2005 October
n=11
0 10
0 10
November
5 n=18 5
November
n= 6
0 60 50 40 30 20 10 0
December
n=194
10
December
n=29
Number of Fish
20 15 10 5 0 20 15 10 5 0 40 30 20 10 0 20 15 10 5 0 10
Number of Fish
10
2006 February
n=13
0 10
March NOT FLOWING
March
n=39
June
n=64
10
June
n= 6
August
n=27
10
August
n= 5
September
n=23
10
September
n= 8
0
0 10 20 30 40 50 70 80 60 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0
0
0 10 20 30 40 50 60 70 80 90 00 10 20 30 40 50 60 1 1 1 1 1 1 1
Total Length(mm)
Total Length(mm)
Figure38
Lengthfrequency distributions of Western Pygmy Perch captured in Rosa Brook and Milyeannup Brook separated by downstream and upstream movement.
66

10
McAtee Brook 2005 October

n=12
Downstream Upstream
0 20 15 10 5 0 10
November
n=54
December
5 n=19
Number of Fish
20 15 10 5 0 20 15 10 5 0 10
NOT FLOWING
2006 February
March NOT FLOWING
June
5 n=18
0 50 40 30 20 10 0 20 15 10 5 0
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0
August
n=155
September
n=34
Total Length (mm)
Figure39
LengthfrequencydistributionsofWesternPygmyPerchcapturedinMcAtee Brookseparatedbydownstreamandupstreammovement.
67

10 8 6 4 2 0 10 8 6 4 2 0 10 8 6 4 2 0 Downstream Migration Upstream Migration
2005 October
n=7
November
n=2
December
n=9
Number of Fish
10 8 6 4 2 0 10 8 6 4 2 0 10 8 6 4 2 0
2006 February
n=0
March
n=1
June
n=13
10 8 6 4 2 0 10 8 6 4 2 0
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0
August
n=0
September
n=0
Total Length(mm)
Figure40
LengthfrequencydistributionsofWesternPygmyPerchcapturedinallmain channel sites using fyke nets; separated by downstream and upstream movement.
68

log10N = 31.38*log10O2 - 32.06 1.0 r2 = 0.99
0.5
0.0
-0.5
-1.0
-1.5 0.98 1.00 1.02 1.04 1.06
log10 mean dissolved O2 (ppm)
Figure41
Relationship between the mean strength of the upstream migration of Western Pygmy Perch within the major flow period (August to December) and the mean dissolved oxygen in the four tributaries during that period. N.B.Datawerelog10transformedandmigrationwasstandardisedforeffort, seetextfordetails.
69

Table5 Correlations between upstream and downstream movement of Western Pygmy Perch in the tributaries of the Blackwood River and prevailingenvironmentalvariablesduringthemigrationperiod.N.B.Datawerelog10transformed.
Log conductivity
Log temperature .686 .314 -.508 .492 .229 .771 -.131 .869 .354 .769 .493 .672
Log conductivity
Log pH
Log O2
Log discharge
Upstream movement
Log pH
-.677 .323 .589 .411 .600 .400 .868 .330 .934 .233 .182 .818 -.573 .427 .406 .734 .262 .831 .311 .689 .991 .088 .958 .185 .422 .722 .279 .820 .988 .098
Log O2
Log discharge
Upstream movement
Downstream movement
70
Nightfish
Habitatassociations The Nightfish was almost exclusively captured within the tributaries of the BlackwoodRiver,whichaccountedfor99%ofcapturesofthisspecies(Figure 42, Appendix 2). As with the Western Pygmy Perch, the species therefore appears to be largely intolerant of conditions in the main channel of the BlackwoodRiverandisreliantontributaryhabitats;particularlywithregards tospawningandrecruitment. Migrationpatterns The highest numbers of Nightfish captured in fyke nets were from Layman Brook(629),largelyasaconsequenceofamassexodusofjuveniles(1020mm TL)fromthissystemduringDecember(Figure42).Similarmovementswere also recorded within Milyeannup Brook and Rosa Brook. The downstream migration is presumably a response to a reduction in discharge at that time with associated water level and habitat decline. Upstream migrations were more ambiguous, however in most systems there were relatively weak upstream migrations in winter and early spring. There is evidence for an earlier and more protracted spawning (and recruitment) period of Nightfish inMilyeannupBrookaslargersizesofthemigratingjuvenileswererecorded inthistributaryinDecember.Forexample,withinMilyeannupBrookthese new recruits ranged in length from 1039 mm TL in this month, compared with1024mmTLinRosaBrookandLaymanBrook(Figures43,44). Migration patterns within the main channel were sporadic, however the majority of fish captured in fyke nets were moving downstream in most months (Figure 45). The only upstream movementsof fish were from those fewindividualscapturedinMarch,JuneandAugust;thelattermonthsbeing priortoitsbreedingperiod(Figures45,46). Nightfishupstreammovementwaspositivelycorrelatedwithmeandissolved oxygen levels during the flow period in the tributaries (Figure 47, Table 6). Mean dissolved oxygen levels in the tributaries were found to account for ~99% (p=0.001) of the variation between the tributaries in the upstream
71
movementofNightfish(Figure47).ThisrelationshipsuggeststhatNightfish may prefer more highly oxygenated streams for spawning, although undoubtedly other habitat parameters of these streams would also be of importance(suchasdegreeofinstreamstructureforeggdeposition)andasa daytimerefugetothisnocturnalspecies.
Nightfish (B. porosa)

120
Rosa Brook
Mean number of fish
100 80 60 40 20 0
NF NF
350
Layman Brook
Mean number of fish
300 250 200 150 100 50 0
DRY DRY DRY
200
Milyeannup Brook
Mean number of fish
150
100
50
30
Mean number of fish
25 20 15 10 5 0
McAtee Brook
NF NF
Oc ry er er er ch tob emb emb brua Mar v c Fe No De Ju ne Au st er gu emb pt Se
Month
Figure42
UpstreamanddownstreammovementofNightfishinthefourtributaries.
72

Nightfish (Bostockia porosa)
10
Rosa Brook
Downstream Upstream
10
Milyeannup Brook
Downstream Upstream
2005 October
2005 October
0 10
0 10
November
5 5
November
0 150 125 100 75 50 25 0
December
60 50 40 30 20 10 0
December
Number of Fish
10
Number of Fish
10
2006 February
0 10
0 10
March NOT FLOWING
March
0 10
June
10
June
0 10
August
10
August
10
September
10
September
0
0 10 20 30 40 50 60 70 80
Total length (mm)
0 10 20 30 40 50 60 70 80 90 00 10 20 30 40 50 60 1 1 1 1 1 1 1
90 10 0 11 0 12 0 13 0 14 0 15 0 16 0
Total length (mm)
Figure43
Lengthfrequency distributions of Nightfish captured in fyke nets in Rosa Brook and Milyeannup Brook separated on upstream and downstream movement.
73

10
Layman Brook
Downstream Upstream
10
McAtee Brook
Downstream Upstream
2005 October
2005 October
0 10
0 10
November
November
0 200 150 100 50 0
0 10
December
5
December
Number of Fish
10
Number of Fish
10
2006 February DRY
0 10
0 10
March
5 5
March NOT FLOWING
DRY
0 10 0 10
June
5 5
June
DRY
0 10 0 10
August
5 5
August
10
10
September
5 5
September
0
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0
0
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0
Total length (mm)
Total length (mm)
Figure44
LengthfrequencydistributionsofNightfishcapturedinfykenetsinLayman Brook and McAtee Brook separated by upstream and downstream movement.
74

Nightfish (B. porosa)
30
Denny Road
Mean number of fish
20
10
30
Milyeannup Pool
Mean number of fish
20
10
NS NS
30
Jalbarragup
Mean number of fish
20
10
30
Quigup
Mean number of fish
20
10
NS NS
to Oc b er No mb emb bru ve c Fe De er er ary rch Ma Ju ne g Au t r us mbe te ep S
Month
Figure45
UpstreamanddownstreammovementofNightfishinthefourmainchannel sitessampled.
75

10 8 6 4 2 0 10 8 6 4 2 0 10 8 6 4 2 0 Downstream Migration Upstream Migration
2005 October
n=1
November
n=1
December
n=2
Number of Fish
10 8 6 4 2 0 10 8 6 4 2 0 10 8 6 4 2 0
2006 February
n=0
March
n=3
June
n=3
10 8 6 4 2 0
August
n=5
10 8 6 4 2 0
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0
September
n=2
Total length(mm)
Figure46
LengthfrequencydistributionsofNightfishcapturedinfykenetsinthemain channelsitesseparatedbyupstreamanddownstreammovement.
76

log10N = 23.49*log10O2 - 24.30 0.6 0.4 r2 = 0.98
0.2 0.0 -0.2 -0.4 -0.6 -0.8 -1.0 -1.2 0.98 1.00 1.02 1.04 1.06
log10 mean dissolved O2 (ppm)
Figure47
RelationshipbetweenthemeanstrengthofupstreammigrationofNightfish within the major flow period (August and December) and the mean dissolved oxygen in the four tributaries during that period. N.B. Data were log10 transformed and migration number was standardised for effort, see textfordetails.
77
Table6
CorrelationsbetweenupstreamanddownstreammovementofNightfishintheBlackwoodRivertributariesandprevailingenvironmental variablesduringthemigrationperiod.N.B.Datawerelog10transformed,**denotescorrelationissignificantatthe0.01level(2tailed).
Log conductivity
Pearson Correlation Sig. (2-tailed) Pearson Correlation Sig. (2-tailed) Pearson Correlation Sig. (2-tailed) Pearson Correlation Sig. (2-tailed) Pearson Correlation Sig. (2-tailed) Pearson Correlation
Log temperature .686 .314 -.508 .492 .229 .771 -.131 .869 .181 .819
Log conductivity
Log pH
Log O2
Log discharge
Upstream movement
Log pH
-.677 .323 .589 .411 .600 .400 .552 .448 .182 .818 -.573 .427 .220 .780 .311 .689 .999** .001 .307 .693
Log O2
Log discharge
Upstream movement
Downstream movement
-.858 Sig. (2-tailed) .142
-.907 .093
.831 .169
-.248 .752
-.380 .620
-.201 .799
78
SouthwesternGoby
Habitatassociations Although Southwestern Goby is typically encountered within estuaries, duringthisstudy,itwasmostcommonlyrecordedwithinmostmainchannel sites;accountingfor~92%ofcapturesofthisspecies(Figure48,Appendix1). Asmallnumberofindividualsofwerealsocapturedinthelowerreachesof Milyeannup Brook (eight) and Rosa Brook (14) (Figure 51). This species is therefore largely reliant on the main channel habitats; an expected finding given it is a known estuarine species and the main channel has become salinised. Migrationpatterns In most months at the downstream main channel sites (receiving most groundwater discharge), the majority of Southwestern Gobies were moving downstream(Figure48).DownstreammovementwasgreatestattheDenny Road site during February, when >100 fish/day were captured. These were largelysmallfishthatwereprobablynewrecruits(1039mmTL)(Figures49, 50). The downstream movement of this cohort continued through to September,withasmallproportionofthesenewrecruitsmovingupstreamin most months. An additional cohort of small fish entered the population in September; suggesting that a second spawning event may have occurred during 2006. The low catches within tributary sites compared to the main channel suggest that the tributaries have unfavourable conditions for this species.Thedownstreammovementoffishwithintributariesonlyoccurred during late spring and early summer, and it is likely that these individuals weremovingbacktothemainchannelforbreedingpurposes. Thegeneraldownstreamtrendinmigrationmaybeexplainedbythefactthat the species is not reputed to have a strong swimming ability. This point is highlighted when, during summer and early autumn, there were greater movements upstream at the sites that had negligible discharge, i.e. the two sites that are upstream of the Yarragadee discharge (i.e. Jalbarragup and Quigup).
79

South-western Goby (A. suppositus)
150
Denny Road
Mean number of fish
100
50
100
Milyeannup Pool
Mean number of fish
80
60
40
20
NS NS
120
Jalbarragup
Mean number of fish
100 80 60 40 20 0
100
Quigup
Mean number of fish
80
60
40
20
NS NS
tob emb emb bru v c Oc Fe No De er er er a ry Ma rc h Ju ne Au st er gu emb t ep S
Month
Figure48
Upstream and downstream movement of Southwestern Goby at the four mainchannelsites.
80

South-west Goby (A. suppositus)
10 Downstream Migration Upstream Migration
2005 October
n=6
0 10
November
5 n=12
0 10
December
n=13 5
Number of Fish
25 20 15 10 5 0 10
2006 February
n=96
March
n=44
0 10
June
n=13
0 10
August
n=19
10
September
n=38
0
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0
Total length (mm)
Figure49
LengthfrequencydistributionsofSouthwesternGobycapturedinfykenets inthemainchannelsitesseparatedonupstreamordownstreammovement.
81

30 25 20 15 10 5 0 30 25 20 15 10 5 0 30 25 20 15 10 5 0 30 25 20 15 10 5 0 30 25 20 15 10 5 0 30 25 20 15 10 5 0 30 25 20 15 10 5 0 30 25 20 15 10 5 0
Rosa Camp Site

2005 October
10.0 7.5 5.0 2.5 0.0
Milyeannup Pool
2005 October
20 15 10 5
Jalbarragup
2005 October
NS November
0 20 15 10
November
10.0 7.5 5.0 2.5 0.0 10.0 7.5 5.0 2.5 0.0 10.0
November
NS December
5 0 20 15 10 5 0 20
December
December
Number of fish
Number of fish
5.0 2.5 0.0 10.0 7.5 5.0 2.5 0.0
Number of fish
2006 February
7.5
2006 February
15 10 5 0 20 15 10 5 0
2006 February
March
March
March
June/July
10.0 7.5 5.0 2.5 0.0
June/July
20 15 10 5 0
June/July
August
10.0 7.5 5.0 2.5 0.0
August
20 15 10 5 0
August
September
10.0 7.5 5.0 2.5 0.0
September
20 15 10 5 0
September
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0 17 0 18 0
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0 17 0 18 0
Total length (mm)
Total length (mm)
Figure50
Lengthfrequency histograms of Southwestern Goby captured using seine netsandelectrofishingatJalbarragup,MilyeannupPoolandDennyRd.NS= notsampled.
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0 17 0 18 0
Total length (mm)
82
South-western Goby (A. suppositus)

10
Rosa Brook
Mean number of fish
10
Layman Brook
Mean number of fish
DRY DRY DRY
10
Milyeannup Brook
Mean number of fish
NF NF
10
Mean number of fish
McAtee Brook
6
ry er er er ch tob emb emb brua Mar Oc ov ec Fe N D
st er ne Ju Augu temb ep S
Month
Figure51
Upstream and downstream movement of Southwestern Goby at the four tributarysites.
83
SwanRiverGoby
Habitatassociations AswiththeSouthwesternGoby,thevastmajorityofcapturesoccurredinthe mainchannel(Figure52,54,Appendices1and2);againreflectingthefactthat itisregardedasanestuarinespeciesthathashaditsinlandrangeincreased duetothesalinisationoftheBlackwoodRivermainchannel. Migrationpatterns Catches of the Swan River Goby in fyke nets were sporadic, but the large majoritycapturedweremovingdownstreaminthemainchannelsites(Figure 52). However, no clear migratory patterns were evident with the exception thatonallbuttwomonthsacrossthefourmainchannelsites,thedownstream migration strength was greater than the upstream movement (Figure 52). This is to be expected in such a slow moving benthic species, and the two occasions where upstream movement was greater than downstream movement was during December at Quigup and in March at Jalbarragup, a period when discharge was reduced and during their known spawning period(Gilletal.1996).Thisissupportedbythepresenceofnewrecruitsin March at Quigup (Figure 53). No notable migrations occurred within tributarysites(Figure54).
84

Swan River Goby (P. olorum)
40
Denny Road
Mean number of fish
30
20
10
40
Milyeannup Pool
Mean number of fish
30
20
10
NS NS
40
Jalbarragup
Mean number of fish
30
20
10
40
Quigup
Mean number of fish
30
20
10
NS NS
to Oc b mb emb bru ve c Fe No De er er er ary rch Ma Ju ne g Au t r u s mb e te ep S
Month
Figure52
UpstreamanddownstreammovementofSwanRiverGobyatthefourmain channelsites.
85

Jalbarragup
2005 October
20 15 10 5 0 20 15 10 5 0 20 15 10 5 0 20
15 10 5 0
Quigup
2005 October
November
15 10 5 0 15 10 5 0 15
November
December
December
Number of fish
Number of fish
15 10 5 0 20 15 10 5 0 20 15 10 5 0 20 15 10 5 0 20 15 10 5 0
2006 February
10 5 0 15 10 5 0
2006 February
March
March
June/July
15 10 5 0
June/July
August
15 10 5 0
August
NS
September
15 10 5 0
September
NS
0 10 20 30 40 50 60 70 80 9 100 110 120 130 140 150 160 170 180 0
Total length (mm)
Figure53
Lengthfrequency histograms of Southwestern Goby captured using seine nets and electrofishing in the two most upstream main channel sites. NS = notsampled.
0 10 20 30 40 50 60 70 80 9 100 110 120 130 140 150 160 170 180 0
Total length (mm)
86
Swan River Goby (P.olorum)

10
Rosa Brook
Mean number of fish
10
Layman Brook
Mean number of fish
DRY DRY DRY
10
Milyeannup Brook
Mean number of fish
NF NF
10
Mean number of fish
McAtee Brook
6
Month
Figure54
Upstream and downstream movement of Swan River Goby at the four tributarysites.
87
WesternHardyhead
Habitatassociations Aswiththeotherestuarinespeciesthatarenowfoundthroughoutthemain channeloftheBlackwoodRiverasaconsequenceofincreasedsalinisation,the WesternHardyheadisalmostcompletelyabsentfromthetributaries(Figures 55,59;Appendices1and2).Ofthe4864captured,onlyfourindividualswere captured from downstream sites in the tributaries; three in Rosa Brook and oneinMilyeannupBrook. Migrationpatterns While the species was common at all main channel sites sampled, relatively few were captured in fyke nets at Milyeannup Pool and at Quigup and this methodmaynotbeconducivetotheircapture.Furthermore,individualswere often sighted near the mouth of nets with few subsequently being captured (Figure 55). However, at the Denny Rd site, there were considerable downstream movements of fish in midlate spring, with both upstream and downstreammigrationsrecordedduringsummer.Minimalmovementswere recorded at most sites during autumn and winter (Figure 55). Similarly, at Jalbarragup, while there was no movement of the species recorded during autumn and winter, there were considerable downstream migrations of fish duringlatespringandearlysummer. LittlerecruitmentofjuvenilefishwasrecordedattheDennyRdsitewhereas considerable numbers of new recruits were captured in late summer and/or early autumn at the other sites as illustrated by clear cohorts in the length frequencyhistograms(Figures5658).Duringthelikelybreeding/recruitment period, i.e. late summer/early autumn, theproportion of new recruits in our catches increased from only a few individuals at Milyeannup Pool to being >50%ofthepopulationatthetwoupstreamsites.Itislikelythatthesalinised environmentofferedbytheseupstreamsitesprovidesthistypicallyestuarine specieswithmorefavourableconditionsforsuccessfulrecruitment.
88
Based on the above findings, an increase in salinity, with a concomitant decrease in discharge in the major groundwater discharge zone, i.e. at sites suchasDennyRdandMilyeannupPool,islikelytoincreasetherecruitment of estuarine species such as the Western Hardyhead as it appears that minimum conductivity favoured for spawning of this species is between ~20003000S/cm.

Western Hardyhead (L. wallacei)
100
Denny Road
Mean number of fish
80
60
40
20
100
Milyeannup Pool
Mean number of fish
80
60
40
20
NS NS
400 300
Jalbarragup
Mean number of fish
200 100
20
Quigup
Mean number of fish
15
10
NS NS
Month
Figure55
Upstream and downstream movement of Western Hardyhead at the four mainchannelsites.
89

10 Downstream Migration Upstream Migration
2005 October
n=18
0 80 60 40 20 0 10
November
n=171
December
n=26
Number of fish
10
2006 February
n=16
0 10
March
n=11
0 10
June
n=1
0 10
August
n= 1
0 10
September
n=10
0
0 10 20 30 40 50 60 70 80 90 00 10 20 30 40 50 60 1 1 1 1 1 1 1
Total length (mm)
Figure56
Lengthfrequency distributions of the Western Hardyhead captured in fyke nets in the main channel sites separated on upstream and downstream movement.
90

50 40 30 20 10 0 50 40 30 20 10 0 50 40 30 20 10 0 50 40
Denny Rd
2005 October
100 80 60 40 20 0 100 80 60 40 20 0 100 80 60 40 20 0 100 80
Milyeannup Pool
2005 October
NS November
November
NS December
December
30 20 10 0 50 40 30 20 10 0 50 40 30 20 10 0 50 40 30 20 10 0 50 40 30 20 10 0
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0 17 0 18 0
Number of fish
Number of fish
2006 February
2006 February
60 40 20 0 150 100 50 0
March
March
June/July
100 80 60 40 20 0
June/July
August
50 40 30 20 10 0
August
September
100 80 60 40 20 0
September
Total length (mm)
Figure57 Lengthfrequency histograms of Western Hardyheads captured using seine netsandelectrofishinginthetwomostdownstreammainchannelsites.NS= notsampled.
0 10 20 30 40 50 60 70 80 90 10 0 11 0 12 0 13 0 14 0 15 0 16 0 17 0 18 0
Total length (mm)
91

Jalbarragup
150 100 50 0 100 80 60 40 20 0 50 40 30 20 10 0 50 40
Quigup
2005 October
2005 October
50 40 30 20 10 0 50 40 30 20 10 0 50 40 30 20 10 0 50 40
November
November
December
December
Number of fish
30 20 10 0 50 40 30 20 10 0 50 40 30 20 10 0 50 40 30 20 10 0 50 40 30 20 10 0
0 10 20 30 40 50 60 70 80 9 100 110 120 130 140 150 160 170 180 0
Number of fish
2006 February
2006 February
30 20 10 0 50 40 30 20 10 0
March
March
June/July
50 40 30 20 10 0
June/July
August
50 40 30 20 10 0
August
NS
September
50 40 30 20 10 0
September
NS
Total length (mm)
0 10 20 30 40 50 60 70 80 9 100 110 120 130 140 150 160 170 180 0
Total length (mm)
Figure58 Lengthfrequency histograms of Western Hardyheads captured using seine nets and electrofishing in the two most upstream main channel sites. NS = notsampled.
92

10
Rosa Brook
Mean number of fish
10
Layman Brook
Mean number of fish
DRY DRY DRY
10
Milyeannup Brook
Mean number of fish
NF NF
10
Mean number of fish
McAtee Brook
6
ry er er er ch tob emb emb brua Mar Oc ov ec Fe N D
Month
Figure59
Upstream and downstream movement of Western Hardyhead at the four tributarysites.
93
PouchedLamprey
Habitatassociations Prior to this study there had been no previous reports of larval Pouched Lampreys(Geotriaaustralis)intheBlackwoodRiver.Duringthisstudy,they wereonlycapturedinMilyeannupBrookandRosaBrook(Figure60).Adults werealsocapturedinfykenetsinRosaBrook(June)andMilyeannupBrook (September), a period that coincides with their upstream migration (see below)(Figure60). This species belongs to the Petromyzontiformes, which are one of the only twosurvivinggroupsofthejawless(agnathan)stageinvertebrateevolution. The absence of jaws and paired fins separates the agnathans from the cartilaginous(sharksandrays)andbony(teleosts)fishes.Whilethereare38 species of extant lampreys, the Pouched Lamprey is the sole member of the Geotriidae and one of only four species of Southern Hemisphere lampreys (Potter 1980). The species is known from southwestern and southeastern Australia, Tasmania, New Zealand and southwestern and southeastern SouthAmerica(Potteretal.1986)andinWAitisfoundinmostoftheriver systems from the Murray River south to approximately the Waychinnicup RivereastofAlbany(Morganetal.1998).Afterapproximatelyfouryears,the microphagouslarva(ammocoete)undergoesaradicalmetamorphosisintoan adult, which possesses eyes, one or two prominent dorsal fins and a tooth bearingsuctorialdisc(Potteretal.1980,Potter&Hilliard1987).Theadultof thespeciesisparasiticandisthoughttofeedonthefleshofteleostfishes(Gill etal.2003). Ammocoetesrequireahighdegreeofshadeandahighabundanceoforganic materialonthesubstrate,factorsthatareknowntoinfluencelarvaldensities (Potter et al. 1986). The metamorphosed juveniles (downstream migrants) however are most often associated with (buried in) sandy substrates that occurinwelloxygenatedwaters(e.g.belowriffles). Thelarvaeareparticularlyvulnerabletohabitatmodificationandrelyonwell oxygenated nonsaline waters that are characterised by shade and organic
94
matter.Thereissubstantialevidencethatlampreysaredeclininginnumbers, particularlyasaresultofthelossoffsuitablehabitatforthelarvae,andthisis evidentwithinsouthwesternAustralianriverssuchastheBlackwoodwhere salinisationandlandclearinghaveresultedinlossoflarvalbeds. While adults and larvae are relatively common in the main channel of a numberofriversystemsinsouthwesternAustralia,e.g.MargaretRiver,itis likely that the higher salinities within the Blackwood River have reduced habitatavailability. Migrationpatterns Thelifecycleiscomplex,withthewormlikelarvalstage(ammocoete)living in burrows below the substrate where they feed on diatoms, detritus and microorganisms.InsouthwesternAustraliaatapproximatelyfouryearsof age (and at approximately 90 mm TL) the ammocoete undergoes metamorphosis with the resultant downstream migrant leaving the river during winter. It is thought that there is a one to two year marine trophic phase, where it presumably feeds on fish and their length increases to approximately500700mmTL.Theadultthenceasesfeeding,reentersrivers and embarks on an upstream migration (moving predominantly at night) duringwinterandspring.Afterspendingapproximately1516monthsinthe river,whentheysurviveoffaccumulatedfatreserves,theadultsspawnand die. During this 1516 month period in the river the adults mature and the males develop a large gular pouch (hence the name pouched lamprey). An enlargement of the oral disc also occurs during this maturation period. The strengthoftheupstreammigrationisvariablefromyeartoyear,anddueto theirnocturnalmigrationbeinginwintertheyareseldomseen.
Fromtopleft(clockwise):Aburrowingammocoete,adultsmigratingupstream,anadult (upstreammigrant)utilisingtheoraldisctomoveupstreamthroughariffle.
95

Pouched Lamprey (G. australis)
10
Milyeannup Brook
Mean number of crayfish
Milyeannup Brook Oct = larvae Feb = larvae Aug = larvae Sept = larvae + 1 adult
10
Layman Brook
DRY DRY DRY
10
McAtee Brook
NF NF
10
Rosa Brook
5
Rosa Brook Dec = adult June = larvae
NF NF
to Oc r r r be mbe mbe ruary arch M b ve ce Fe No De st er ne Ju Augu temb p Se
Month
Figure60
Upstream and downstream movement of Pouched Lampreys in the four tributaries.N.B.Thisfigurerepresentsammocoeteandadultcaptures.
96
EasternMosquitofish
Habitatassociations The introduced Eastern Mosquitofish was far more abundant within main channel sites than tributaries, where they were essentially confined to shallow,littoralhabitats(Figures61,62,Appendices1and2).Thespeciesis now widespread throughout the Blackwood catchment where it dominated catches in two previous studies of the fishes in this system (Morgan & Gill 2000,Morgan&Beatty2005).Approximately82%ofallindividualscaptured duringthelatterstudywerefrommainchannelsites. The species is originally from Eastern North America and is now one of the most widely distributed introduced freshwater fish species in the world. Althoughrelativelysmall,thespeciesisaggressiveandfinnipsnativespecies (Gill et al. 1999). It generally prefers degraded systems, particularly those withlowflowssuchasartificialwetlandsandirrigationdrains. Migrationpatterns With the exception of a few Eastern Mosquitofish moving downstream in June, this species was only ever captured in fyke nets in the main channel sitesduringlatesummerandearlyautumn,aperiodthatcoincideswithboth lowflowsandtheirbreedingperiodinsouthwesternAustralia(Pen&Potter 1991).Whilethissuggeststhatmovementmayberestrictedtothesemonths, thelowcatchesinfykenetsmayimplythatthespeciesisnotreadilycaptured using this technique. Within the tributaries, they were only ever captured duringDecemberinMcAteeBrook(Figure62).
97

Mosquitofish (G. holbrooki)
30
Denny Road
Mean number of fish
20
10
30
Milyeannup Pool
Mean number of fish
20
10
30
Jalbarragup
Mean number of fish
20
10
30
Quigup
Mean number of fish
20
10
Month

Figure61 Upstream and downstream movement of Eastern Mosquitofish at the four mainchannelsites.
98
Mosquitofish (G. holbrooki)

10
Rosa Brook
Mean number of fish
10
Layman Brook
Mean number of fish
DRY DRY DRY
10
Milyeannup Brook
Mean number of fish
NF NF
10
Mean number of fish
McAtee Brook
6
Month
Figure62
Upstream and downstream movement of Eastern Mosquitofish at the four maintributarysites.
99
Goldfish
Habitatassociations During this study Goldfish were only captured within crayfish traps at the DennyRdsiteonthemainchannel.Theywerepreviouslyrecordedthereby Morgan & Beatty (2005), who also recorded this species from another Blackwood tributary; Red Gully. As with many introduced species, this species thrives in disturbed habitats such as artificial lakes or eutrophic waters. Migrationpatterns Due to nocapturesinfykenets,noconclusionsregardingmigrationsin this system can be drawn. However, this species is known to be increasing its distribution in the southwest with a control programme recently been implemented for a selfmaintaining population in the Vasse River. This specieshasbeenshowntoremineralisenutrientsintothewatercolumnbyits feedingactivityandthusmayexacerbatealgalblooms.
100
RainbowTrout
Habitatassociations This specieswas recordedinMilyeannup Brook inspring2005(seeTable 7) and in summer 2006 in McAtee Brook (Appendix 2). Rainbow Trout are stocked by the Department of Fisheries into the Blackwood River and its tributaries, and thus its occurrence throughout the catchment is largely a resultofthisstockingregime.Between2000and2005,over500000Rainbow TroutfrywerestockedintotheBlackwoodRivercatchment.Tributariesthat havebeenstockedincludeMilyeannupBrook,CarlottaBrook,HestersBrook, NannupBrook,StJohnBrook,RedGully,GeegellupBrook,EllisCreek,Rosa Brook and Adelaide Brook. The Recreational Freshwater Fisheries Stakeholder Subcommittee terminated the stocking of Rosa Brook and AdelaideBrookin2005,andMilyeannupBrookstockingceasedfollowingthe stockingof10000fishin2005,largelyattheadviceofthisstudy.Onlylimited natural recruitment of this species occurs within southwestern Australian streams, and the low catches of this species during this study suggests that survivorshipofstockedfryisminimal(Figure63).Howeverasmallnumber oflargerfishwereobservedinMilyeannupPool.Althoughsurvivorshipmay appear to be low, the threat posed by this introduced species is substantial, particularlywhendealingwithrarespeciesthatarerestrictedindistribution and have very short lifecycles; such as the Mud Minnow and Balstons PygmyPerch. Migrationpatterns Following the stocking of Rainbow Trout into Milyeannup Brook in September 2005, a large number were caught using an electrofisher. In subsequent months, these fish were caught in fyke nets where most were captured moving downstream where they presumably move into the main channel. The species was captured with other native fishes, including juvenileBalstonsPygmyPerchandMudMinnowsandposedaseriousthreat to these species, in terms of competition for habitat and predation. As the stocking of streams that are adjacent to Milyeannup Brook, such as McAtee Brook, Red Gully and St John Brook, is likely to continue, the movement
101
patterns, survivorship and diet of stocked Rainbow Trout needs to be examinedsoastodeterminetheirimpactontherarespeciesinthesesystems. Furthermore,thelevelofrecreationalfishinginthisareashouldbequantified todetermineifstockingthesesystemsiswarrantedfromacostbenefitpoint ofview.
Rainbow Trout (O. mykiss)

10
Rosa Brook
Mean number of fish
10
Layman Brook
Mean number of fish
DRY DRY DRY
10
Milyeannup Brook
Mean number of fish
NF NF
10
Mean number of fish
McAtee Brook
6
Ju
ne
Au
r st gu embe pt Se
Month
Figure63
Upstream and downstream movement of Rainbow Trout in the four tributaries.
102
Marron
Habitatassociations Although the Marron are found in considerably greater numbers within the main channel of the Blackwood River, they were also captured in all tributarieswiththeexceptionofLaymanBrook(Figures6466,Appendices1 and 2). This is a species generally regarded to favour larger, permanent aquaticsystems(Austin&Knott1996)thusexplainingitsgreaterabundance inthemainchannelsitescomparedtotributaries. Migrationpatterns BothupstreamanddownstreammigrationsofMarronwereobservedduring fyke netting in the main channel sites and within the tributaries (Figures 64 and65). Marronpopulationanalysis Using catches in crayfish trap data, there was an overall greater CPUE in those main channel sites receiving Yarragadee Aquifer discharge (1.64 trap1 0.22S.E.)comparedtothoseupstreamofthedischarge(1.43trap10.21S.E.) although this was not statistically significant (p = 0.496). Catches per unit effortpermonthareshowninFigure66withthegreatestcatchesoccurringin July and August. Sites within the Yarragadee Aquifer discharge zone had greater catches of Marron in October (significant: p = 0.019), December, February and July than those upstream of the zone with this trend being reversedinAugustandSeptember.Thissuggestedthattheremayhavebeen moreactivity(i.e.foraging)duringthelowrainfallmonthsatsitesreceiving moregroundwaterdischargeinsummerthanthoseupstream. Although the sampling regime employed could not specifically quantify breeding and recruitment success of the Marron population, the wide range ofagecohorts(includingsimilar0+recruitsbetween1020mmOCLinboth zones) observed in the lengthfrequency distributions suggested that the Marron populations in the main channel sites were similar in structure (Figure67).However,moreintensiveexaminationoftheMarronpopulations within the two zones would be required to specifically compare population
103
health (e.g. productivity based on growth rates, densities, breeding and recruitmentrates). The spawning period of Marron in the Blackwood River appeared to be betweenJulyandSeptemberassuggestedbythedeclineintheproportionof femaleswithmature/ripeovaries (Figure68).This timing isconsistent with previousstudiesofthisspecieselsewhere(Beattyetal.2003,2005a). InsufficientnumbersoffemaleMarronwereretainedtocomparethelengthof first maturity of Marron in the two zones (in order to reduce the impact of removing large numbers of the breeding population from the river) so femalesfromallsiteswerepooledintheanalysis.Thelengthatwhich50% (L50) of female Marron matured in the Blackwood River was 55.6 mm OCL which approximates the previous (i.e. prior to 2007 recreational season) minimum legal size for capture of 76 mm carapace length (CL) (Figure 69). Thissizeatmaturityoffemalesislargerthanthatrecordedforthisspeciesin WaroonaDam(32.1mmOCL,Beattyetal.2003)butsmallerthanintheHutt River (69.3 mm OCL, Beatty et al. 2004), at the northernmost extent of its range; again reflecting the plasticity in its biology (see Beatty et al. 2004). However,duetotherelativelylownumbersoffemalesretainedandusedin theanalysis,thissizeatmaturityrequiresfurthervalidation. Although not statistically significant (probably due to sample size, i.e. number of traps deployed), the slightly higher CPUE of Marron within the major groundwater discharge zone compared with sites upstream is understandable given that recreational catch rates of Marron have recently beenpositivelyassociatedwithwaterlevels(Molonyetal.unpublisheddata) andseasonalpredictionsofrecreationalcatchesarebasedonmodellingwith future rainfall (i.e. a prediction of river flow). This positive relationship betweenMarronandwateramountisprobablyduetoincreasedrecruitment success(andprobablyoverallproductivity)thatincreasedwaterlevelsallow duetoincreasedhabitatavailability(increasingjuvenilesurvivalbyreducing competitionforspace)andfoodresources(e.g.allochthonousorganicmatter inputduetoincreasedbankinundation). Increased summer river flow in particular could result in increased productivityasthisseasonoccursafterthepeakspawningperiod(Figure68) and coincides with peak juvenile release (early summer in the Blackwood River allowing for a 1015 week attachment period to females). Marron growth is most rapid in this early period of life (Beatty et al. 2004) and they are also most vulnerable to interspecific (e.g. Rainbow Trout, Freshwater Cobbler)andintraspecific(i.e.adultMarron)predation.Therefore,giventhat considerablecontributionofsummerflowoftheBlackwoodRiverisderived
104
fromYarragadeegroundwater(attimesupto100%ofthetotalsummerflow indrysummersisderivedfromcombinedgroundwaterdischarge,Strategen (2006), substantial reduction in the minimum summer flow in the main channel of the Blackwood River may result in reduced productivity of the Marron population occupying this stretch of the Blackwood River (due to reducedjuvenilesurvivorshipandresourceavailability).Thismaytherefore lead to reduced recreational Marron captures in this zone. An ongoing monitoring program of the Marron population examining relative abundances and productivity should be implemented if such reductions in dischargeoccur.
Marron (C. cainii)

200
Denny Road
100 80 60 40 20 0
40
Milyeannup Pool
30
20
10
NS
NS
40
Jalbarragup
30
20
10
80
Quigup
60
40
20
NS
NS
Month
Figure64
Upstream and downstream movement of Marron at the four main channel sites.NS=notsampled.
105
Marron (C. cainii)

10
Milyeannup Brook
10
Layman Brook
DRY DRY DRY
10
McAtee Brook
NF NF
10
Rosa Brook
NF NF
Month
Figure65
UpstreamanddownstreammovementofMarroninthefourtributaries.NF =notflowing.
106

Sites receiving Yarragadee discharge Sites upstream of Yarragadee discharge
Catch per unit effort (marron/trap)
*
2
0
ly ch er ry st r be Ju ob ua ar gu ce Au em Se pt m br ct M be r
De
Fe
Month
Figure66
Catch per unit effort (CPUE, Marron.trap1) of Marron in the Blackwood River.N.B.*denotesasignificantdifferencebetweentheCPUEzonesinthat monthatp<0.05.
107

10 8 6 4 2 0 10 8 6 4 2 0
October
October
n = 87
Sites receiving Yarragadee discharge Sites upstream of Yarragadee discharge
December
n = 46
oct up
Number of Marron
10 8 6 4 2 0 10 8 6 4 2 0 10 8 6 4 2 0
February
n = 56
August
n = 78
September
n = 21
0 10 20 30 40 50 60 70 80 90 100
Orbital carapace length (mm)
Figure67 LengthfrequencydistributionsofMarronoverthesamplingmonthswithin the two zones. N.B. the dashed line indicates the approximate minimum legalsizeforrecreationalfishingof80mmCL.
108

July n=3
100 80 60 40 20 0
100 80 60 40 20 0
August
n = 39
Percentage contribution (%)
100 80 60 40 20 0
September
n = 14
100 80 60 40 20 0
October
n = 36
100 80 60 40 20 0
1
December
n = 17
Gonad Stage
Figure68 PercentagesofovarianstagesoffemaleMarronoverthedifferentsampling monthsintheBlackwoodRiver.N.B.stagesIIIareimmature,stagesIIIVII aremature(VII=berriedfemale).
109

Mature ovaries (stage III-VII) Immature ovaries (stage I-II) Median maturity line Lower 5% confidence interval Upper 95% confidence interval
2 100
Percentage mature (%)
75
50
25
0 10 20 30 40 50 60 70 80
Orbital carapace length (mm)
Figure69 Percentage contributions of stages I/II (i.e. immature) and IIIVII (i.e. maturing / mature) in gonadal development in sequential 5 mm OCL intervalsoffemaleMarronintheBlackwoodRiverinJulyandAugust2006. The logistic curve was fitted to the percentage of Marron with gonads at stages IIIVII. N.B. L50 is shown by the junction of the dashed vertical and horizontallines(55.6mmOCL).
110
Gilgie
Habitatassociations Although found in both main channel and tributaries sites, Gilgies were found in higher numbers in the latter habitats (Figures 70, 71, Appendices 1 and 2). Although this species occupies almost the full range of freshwater systemsinsouthwesternW.A.,itisoftenassociatedwithsuchsmallstreams (Austin&Knott1996).Itisalsoaspeciesabletoliveinbothpermanentand temporarysystemsduetoitsabilitytoburrowintothewatertabletoescape drought.Italsomaturesatasmallsizeandisbelievedtohavetheabilityto breedmultipletimesoverspringandsummer(Beattyetal.2005)allowingit toproliferateinseasonallyinundatedsystems(seealsosection2). Migrationpatterns Most of the movement in the main channel was recorded during winter (Figure71);possiblyasaprecursortobreedingwithinthetributaries.These movements can be traced into the tributaries with substantial upstream migrationsoccurringinwinterandspring(Figure70).Analysisintemporal trends in gonadal development will aid in elucidating whether these migrations were indeed for breeding. Migrations into the tributaries would provide small juveniles with relatively safe habitats away from large predatorssuchasFreshwaterCobblerandMarron.

111
Gilgie (C. quinquecarinatus)

10
Milyeannup Brook
10
Layman Brook
DRY DRY DRY
30
McAtee Brook
25 20 15 10 5 0
NF NF
30
25 20 15 10 5 0
Rosa Brook
NF NF
ry er er ch mb emb brua Mar to ve c Oc Fe No De r be Ju ne g Au t r us mbe pte Se
Month
Figure70
UpstreamanddownstreammovementofGilgiesinthefourtributaries.NF= notflowing.
112

Gilgie (C. quinquecarinatus)
10
Denny Road
30
Milyeannup Pool
20
10
NS
NS
20
Jalbarragup
10
10
Quigup
NS NS
ry er er er ch tob emb emb brua Mar Oc ov ec Fe N D st er ne Ju Augu temb ep S
Month
Figure71
Upstream and downstream movement of Gilgies at the four main channel sites.NS=notsampled.
113
RestrictedGilgie
Habitatassociations TheRestrictedGilgiewasnotcapturedinfykenetsinthemainchannelsites sampled during this study; however Morgan & Beatty (2005) recorded two individualsofthespeciesinthemainchannelattheGreatNorthRdcrossing. In this study, we recorded the species during electrofishing and/or seine netting in low numbers at Milyeannup Pool, Jalbarragup and Quigup (Appendix 1). They were also recorded during electrofishing in McAtee Brook,PoisonGullyandMilyeannupBrookandMorgan&Beatty(2005)(see alsoSection2)capturedthespeciesinRosaBrook(Appendix2).Thisspecies isgenerallyassociatedwithsmallstreamsystemsandisalsoabletosurvive in seasonally inundated systems due to its ability to burrow into the water table(Austin&Knott,1996). Migrationpatterns Duetothelimitedmovementsofthespeciesrecordedduringthefykenetting (Figure72) itisnot possibletomake inferenceson migrationpatternsof the species.Furthermore,apartfromgeneticstudies(Austin&Knott1996),there has been limited research into the biology and ecology of this restricted species(seeSection2).

114

Restricted Gilgie (C. crassimanus)
10
Milyeannup Brook

10
Layman Brook
DRY DRY DRY
10
McAtee Brook
NF NF
10
Rosa Brook
NF NF
ry er er er ch tob emb emb brua Mar Oc ov ec Fe N D st er ne Ju Augu temb ep S
Month
Figure72
Upstream and downstream movement of Restricted Gilgies in the four tributariessampled.NF=notflowing.
115
Koonac
Habitatassociations TheKoonacwasnotrecordedinfykenetsinthemainchannelsitessampled duringthisstudy;howevertheywerecapturedusingseines/electrofishingat Jalbarragup (Appendix 1). Morgan & Beatty (2005) recorded numerous individuals of the species in a number of main channel sites within the YarragadeeDischargeZone.Koonacswereoccasionallycapturedinfykenets in the lower section (Figure 73) and by electrofishing in the upper section (Appendix2)ofMilyeannupBrook.Itwasalsorecordedononeoccasionin fykenetsinRosaBrookandononeoccasionduringelectrofishinginMcAtee Brook(Figure73,Appendix2).AswiththeGilgie,itisfoundinasimilarly wide range of permanent and temporary aquatic systems throughout the southwestofW.A.astheGilgiebutismostcommonlyassociatedwithlentic wetlands(Austin&Knott1996)(seealsoSection2). Migrationpatterns Due to low numbers recording using fyke nets there were no discernable trendsevidentinmigrationpatterns.Thereisalsonopublishedworkonthe ecologyorreproductivebiologyforthisspecies;however,itmaybesimilarto that of the Gilgie (Beatty et al. 2005) given that it occupies a similarly wide rangeofpermanentandtemporaryaquaticsystemsthroughoutitsrange.

116
Koonac (C. preisii)

10
Milyeannup Brook
10
Layman Brook
DRY DRY DRY
10
McAtee Brook
NF NF
10
Rosa Brook
5
NF NF
ry ch tob emb emb brua Mar v Oc ec Fe No D er er er Ju ne g Au t r us mbe te ep S
Month
Figure73
UpstreamanddownstreammovementofKoonacsinthefourtributaries.NF =notflowing.
117
MILYEANNUPBROOKCASESTUDY
Samplingregime(MilyeannupBrook) Duringthisstudy,itbecameapparentthatMilyeannupBrookisasignificant system from a conservation perspective and warranted further investigation. Thissectiondetailstheseinvestigations.MilyeannupBrookwassampledfor fish migrations at a total of three sites: at the confluence of the Blackwood River in winter and spring 2006 at Brockman Hwy (permanent flow, ~300 m from the confluence with the Blackwood River) on each sampling occasion throughoutthestudy,andatBlackwoodRd(ephemeralsite,~3700mfromthe BlackwoodRiver)duringspringandsummer2005(Table7,Figure74). In addition to understanding the patterns of fish movement in Milyeannup Brook, this system was intensively sampled during the dry period in summer/autumn 2006 to determine the extent of its permanent flow due to YarragadeeAquiferdischargeandthedistributionpatternsoffishduringthe timeofreducedflow.Atotalofeightadditionalsites weresampledforfish andcrayfishdensitiesinthesummer(February)andautumn(March)of2006 of which two were completely dry (i.e. no flow or remnant pool present) (Table 7, Figure 74 and 75). At each site, a GPS was used to record the coordinatesandamap(Figure1)oftheseandthemigrationsitessubsequently producedusingMapInfoTMandoverlayedontoanaerialphoto(Departmentof Land Administration) (note that the uppermost sites Mil 12 and Mil 13 on Milyeannup Rd are not shown due to loss of detail of the other sites due to scale)(seeFigure1fordetails). At each of the dryseason sites, three replicate areas totalling up to 650 m2 weresampledforfishandfreshwatercrayfishusingabackpackelectrofisher (setonaminimumpowersoasnottocompromisethehealthofresidentfish). Ateachreplicatesite,5mseinenets(meshwidth2mm)wereusedtoblock upstreamanddownstreamfishescape.Allfishandcrayfishspeciesrecorded within each replicate area were identified, counted and a subsample measuredtothenearest1mmTLbeforebeingpromptlyreleased.Densities( 1S.E.)werecalculatedforeachspeciesrecordedateachsite. Densities of Balstons Pygmy Perch in Milyeannup Brook were previously determined viaelectrofishingatbothMil2and Mil 3 (representing two sites within species permanent range) during early April 2005 (Morgan & Beatty 2005).Thesameelectrofishingtechniquewasundertakenasdescribedforthe abovesummer2006distributionalsurvey.
118

ExamplesofvarioushabitatssampledinMilyeannupBrook;BalstonsPygmyPerch(centre).
119
Seasonal migration Summer quantitative Winter/spring quantitative
Mil1 Mil2 Mil3 Mil4 Mil5 Mil6 Mil7

~1300m summer limit of Balstons Pygmy Perch
PG1
~2000m limit of other species
~2500m flow limit
Mil8 PG2
0 0
Figure74
1 Km
2 2
Mil9 Mil10 Mil11
SitessampledforfishandfreshwatercrayfishinMilyeannupBrook(Mil)andPoisonGully(PG)(aerialphotofromDepartmentofLand Administration).
120
RESULTS(MilyeannupBrook) ThemigrationdataforMilyeannupBrook(seemigrationsectionforadetailed account of individual species) showed that this system is the only tributary that houses a selfsustaining population of the vulnerable Balstons Pygmy Perch.ThelimitofthepermanencyofflowinMilyeannupBrookinFebruary 2006wasapproximately2500mfromitsconfluencewiththeBlackwoodRiver (Figure 74). The limit of upstream fish distribution was found to be approximately2000mfromtheconfluencewiththeBlackwoodRiver(Figure 74,Table7).FishwererecordedatMil9andMil10(Figures74and75),the majorityofwhichwerejuvenileWesternPygmyPerch,NightfishandWestern Minnow,however,itwasapparentthatthepoolswerenotpermanentdueto very shallow depth and thus the fish would not have survived the ensuing lowrainfallmonths. Much of the section of permanent flow in summer is very shallow and the fishes occupying sites Mil 4 Mil 6 included Western Minnow, Western Pygmy Perch, Nightfish, and Mud Minnow. Of particular note is that the Balstons Pygmy Perch was not found upstream of Mil 3 (~1000 m from the Blackwood River confluence) and therefore its uppermost distribution in the driestmonthsduring2006laybetween10001300mfromtheBlackwoodRiver confluence (Figure 75). The failure of the Balstons Pygmy Perch to utilise a greater proportion of the permanent, groundwater fed stream length was probably the unsuitability of the shallow habitat in the upper ~40% of permanent streamlength and requires an examination of interannual variation. ThedensityofBalstonsPygmyPerchatMil2andMil3wasfoundtobe0.09 m2 (0.01). Based on an average channel width utilisation (23 m) and an actualstreamlength(duetomeanders,additional30%of1300m)resultingin anestimatedsummerpopulationinMilyeannupBrookof~380m2(42). As noted, this was a relatively atypical climatic year for the region and the interannual variation in fish distribution in Milyeannup Brook needs to be elucidatedbysubsequentdryseasondistributionalsampling. DISCUSSION(MilyeannupBrook) BiologicalSummary This study has confirmed that Milyeannup Brook stands out from a conservation perspective. It houses the only viable population of the Vulnerable(EPBCAct1999)BalstonsPygmyPerchintheBlackwoodRiverand is also where the most prolific migrations of Mud Minnow were recorded. The Balstons Pygmy Perch was found to undertake strong upstream
121
migrationsinwinterandspringtouppersectionsofthesystemaspartofits reproductive cycle. The probable spawning habitats of this species in the upper, sections of Milyeannup Brook (i.e. upstream of Milyeannup Rd) need to be determined as these seasonal areas may also be susceptible to groundwater level changes (e.g. changes in the period of inundation of floodedareasduetoloweringofsuperficialaquifers). OfmajorimportanceisthatduringthedriestmonthsBalstonsPygmyPerch was not found upstream of Mil 3 its uppermost distribution in the driest months was between 10001300m from the Blackwood River confluence (Figure 74). The failure of the Balstons Pygmy Perch to utilise a greater proportion of the permanent, groundwater fed stream length was probably the unsuitability of the shallow habitat in the upper ~40% of permanent streamlength. As a few Balstons Pygmy Perch were captured in Milyeannup Pool at the confluenceofMilyeannupBrookandtheBlackwoodRiver,someindividuals mayutilisethemainchannelnearthemouthofthebrookperiodicallybefore reentering it to spawn (see section on Balstons Pygmy Perch), however it appears that, during the dry period, the perennial section of Milyeannup Brook(reliantonYarragadeeAquiferdischarge)representsacrucialrefugefor this species. Furthermore, although the length of this perennial section is ~2500 m (in 2006),onlythelower~1300m(~52%) is suitable for inhabitation by this species; possibly due to inadequate depth of upper sections (i.e. generally<0.5m). Predictedhydrologicalchangesduetogroundwaterreduction ThelowersectionsofbothMilyeannupBrookandPoisonGullyareextremely vulnerable to surface groundwater reductions as they are areas of direct dischargefromtheYarragadeeAquifer(Strategen2006).Indeed,basedonthe interpreted(takingintoaccountavailablegeologicalinformationoftheregion) predictionsbyStrategen(2006),theproposed45GL/yrextractionbytheWater Corporationwoulddirectlyleadtodrawdownsofwatertableofupto23m in Milyeannup Brook, and up to 12 m in Poison Gully. However, the estimateddrawdownsfromcombinedregionaluseandtheWaterCorporation proposalareforwatertablereductionsofboththosesystemsofbetween35m (Strategen 2006). It is therefore predicted that the summer discharge from boththesesystemswillreduceby30%.Basedonthesepredictions,thelength ofbaseflowinthestreamsduringdrymonthsisexpectedtoreduceby: upto1500mfromthecurrentsource,2500mfromtheBlackwoodRiver,to 1000mfromtheBlackwoodRiver(p741,Strategen2006) and:
122
severalhundred metresinPoisonGully, from the currentposition 3500m upstream from the confluence of the Blackwood River (p 741, Strategen 2006). This 60% reduction in the base flow length in Milyeannup Brook has considerableimplicationsfortheprevailingaquaticfaunaandparticularlyfor BalstonsPygmyPerchthat,asmentioned,usethishabitatasacrucialsummer refuge. Of major concern is the combined, synergistic effect of habitat reduction in Milyeannup Brook through summer stream length reduction coupled with predicted main channel water quality changes. That is, the Balstons Pygmy Perch currently appears to have only limited usage of the main channel (appearing to be restricted to reaches near the confluence of Milyeannup Brook, e.g. Milyeannup Pool) probably due to change in water quality, particular, elevated salinities. Due to the expected reduction in Yarragadee Discharge into the main channel due to future regional use and the Water Corporations proposal, the dry period salinity is expected to increaseintheBlackwoodRiver(~14%,Strategen,2006). Therefore,shouldthecurrentrefugeinMilyeannupBrookbecomeunsuitable ashabitatreduces,thespecieswouldbeforcedtoretreatintothemainchannel thatmayhavewaterqualityparameters(particularlysalinity)thatexceedthis speciestolerancethuseliminatingitfromtheBlackwoodRiverentirely.Itis therefore of crucial importance to determine the salinity tolerances of the native freshwater species (including the Balstons Pygmy Perch) in order to assess their viability under the predicted increased summer salinity in the YarragadeeAquiferdischargezone.
123
Mil 4
Mil 5
Mil 6
Mil 7
Mil 9
Mil 10
Figure 75
Sites sampled in Milyeannup Brook in summer 2006 to determine fish and freshwater crayfish distributions.
124
Table7
ThesitessampledinMilyeannupBrook,samplingtimes,anddensitiesandtotalnumbersoffishandcrayfishrecorded.
Continued next page

Season Site Lat Long Total Mean Species Density m2 (total number captured) in Milyeannup Brook using Seine and/or Electrofishing. area sampled Native Fishes Feral Freshwater Crayfish (m2) Fishes
Nannatherina balstoni Galaxias occidentalis Edelia vittata Bostockia porosa Galaxiella munda Afurcagobius suppositus Oncorhynchus mykiss Cherax cainii Cherax quinquecarinatus Cherax preisii Cherax crassimanus
Mil 1 All seasons Mil 2 All seasons Mil 3 All seasons Autumn 2006 Mil 4
34.09089
115.5661
SEE MIGRATION SECTION 34.0933 115.56557
SEE MIGRATION SECTION 34.09882 115.5699
SEE MIGRATION SECTION
34.10128
115.570 20 125 0.072 (9) 1.25 (20) 0.400 (50) 0.200 (4) 0.104 (13) 0.100 (2) 0.064 (8) 0.100 (2) 0.024 (3) 0.700 (14) 0.056 (7) 0.150 (3) 0.008 (1)
Summer 2006 Winter 2006 34.10403 115.57085 Mil 5 Summer 2006 34.10682 115.56996 Mil 6 Summer 2006
30
0.833 (25)
0.033 (1)
0.033 (1)
0.033 (1)
0.033 (1)
0.300 (9)
20
0.600 (12)
0.300 (6)
0.100 (2)
125
Season Site Lat Long
Total Mean Species Density m2 (total number captured) in Milyeannup Brook using Seine and/or Electrofishing. area sampled Native Fishes Feral Freshwater Crayfish (m2) Fishes
Nannatherina balstoni Galaxias occidentalis Edelia vittata Bostockia porosa Galaxiella munda Afurcagobius suppositus Oncorhynchus mykiss Cherax cainii Cherax quinquecarinatus Cherax preisii Cherax crassimanus
Mil 7 Autumn 2006 Mil 8
34.10897
115.57004 25
34.11852
115.5683 DRY
Summer 2006 34.12135 115.56952 Mil 9 Summer 2006 Mil 10 34.12165 115.56929 Summer 2006 Winter 2006 Mil 11 All seasons Spring 2005 Mil 12 Spring 2005 Mil 13 34.17172 115.57614 Spring 2005 Summer 2006
37.5
0.213 (8)
0.213 (8)
7.5 150 34.1234 115.5698
0.133 (1)
0.533 (4)
SEE MIGRATION SECTION 650 34.17118 115.56968 45 0.044 (2) 0.089 (4) 0.012 (8) 0.012 (8) 0.012 (8) 0.006 (4) 0.006 (4) 0.049 (32) 0.010 (7)
207.5 DRY
0.198 (41) 126
CONCLUSIONSANDRECOMMENDATIONS
Salinisation of the Blackwood River has resulted in the habitat availability for the freshwaterfishesbecomingdrasticallyreduced(Morganetal.2003).Manyarenow restrictedtotheforestedtributarieswithinthelowercatchmentandinthesectionof the main channel where salinity is reduced as a consequence of groundwater dischargefromtheYarragadeeandLeedervilleaquifers. Thisstudyexaminedpopulationdemographicsandmigratorybehaviouroffishesin and around this groundwater discharge zone on eight occasions between October 2005 and September 2006. A variety of sampling methods were utilised including fykenetting,seinenetting,trappingandelectrofishing. Substantialdifferencesinfishdensitiesandmigrationpatternsexistedbetweenand within the main channel and major tributaries. Main channel sites receiving most groundwaterdischarge(i.e.fromboththeLeedervilleandYarragadeeaquifers)had much greater abundances of nonsalt tolerant freshwater native species than those sites upstream of major groundwater discharge. This suggests that fresh groundwater input in summer (when many tributaries cease to flow or dry completely), may be enabling those species to continue to survive in the salinised mainchannel. TheconsiderableupstreammigrationsofFreshwaterCobblerinmainchannelsites, where the vast majority of captures occurred, were highly correlated to summer discharge. This species is considered to be ideal for longterm monitoring of river connectivity such as assessing the adequacy of discharge over riffles to allow its migration. Thetimingandstrengthsoffishmigrationsdifferedsubstantiallybetweentributaries fortheWesternMinnow,NightfishandWesternPygmyPerchandtributarieswere foundtobethemajorspawninghabitatsforthesespecies.Thesectionofthemain channel that receives the most groundwater discharge and perennial tributaries appear to act as a summer refuge when the contraction or drying of most of these tributariesoccurs. Environmental variables during the peak flow period explained differences in the strength of migrations between tributaries for some native freshwater species. For example,downstreamandupstreammigrationstrengthsoftheWesternMinnowin thefourtributarieswerehighlycorrelatedwithstreamdischargewhereasupstream migrations of Western Pygmy Perch and Nightfish were correlated with dissolved oxygenlevels.
AslightlyhigherrelativeabundanceofMarron(althoughnotstatisticallysignificant) was recorded within sites receiving most groundwater discharge (i.e. both Leederville and Yarragadee Aquifer discharge) than sites upstream. Marron recreational catches are positively correlated with river flow and this has implicationsfortherecreationalfisherywithintheBlackwoodRivershouldsummer flowsbereduced. Milyeannup Brook is of critical conservation importance as it houses the only populationoftheBalstonsPygmyPerchintheBlackwoodRivercatchment(listedas Vulnerable under the EPBC Act 1999). The perennial flows of this system, as a consequenceofgroundwaterdischarge,provideacrucialrefugetoBalstonsPygmy Perch with it being the only tributary of the Blackwood River in which this fish reproduces.WhilethisspeciesmovesintotheupperreachesofMilyeannupBrookto breed,itretreatedbacktowithin~1300moftheBlackwoodRiverinthedrymonths; suggestingthatonly~52%ofthe~2500mbaseflowstreamlengthcontainedsuitable habitat(e.g.adequatedepth)forthisspecies.Thisperennialtributaryalsoprovided important spawning habitat to other freshwater species and fostered earlier recruitmentofsomespecies.ThelowbaseflowpopulationoftheBalstonsPygmy Perch results in it being particularly vulnerable to habitat decline; particularly if summer base flow to this tributary is reduced significantly and main channel summerwaterqualityalsodeclines. Anumberofkeyknowledgegapsandrecommendationspertainingtotheecologyof thefishcommunitieshavebeenidentifiedinthisstudyincluding: The degree of interannual variation in migration patterns and groundwater relianceofthesecommunitiesshouldbedeterminedbyprecisereplicationof themethodsdescribedhere;thiswouldrepresentasolidbaselinedatasetfor anongoingmonitoringprogramme. Salinitytolerancesofthesespeciesshouldbedeterminedinlightofpredicted potential further increased main channel salinities due to summer flow reductions to determine critical thresholds for maintenance of summer populations. Critical riffle zones in the Blackwood River need to be identified and Freshwater Cobbler migration ability precise determined as a basis for ongoingmonitoringofriverconnectivity. Poison Gully should be included in future determination of interannual variation in migration patterns to determine its ecological significance in termsofaquaticfauna. TodeterminewhethertheBlackwoodRivermainchanneliscausingbiological isolation due to elevated salinities, the degree of genetic isolation of specific speciesoffishandcrayfishbetweentributariesshouldbedetermined.
128
REFERENCES
Austin, C. M. and Knott, B. (1996). Systematics of the freshwater crayfish genus Cherax Erichson (Decapoda: Parastacidae) in southwestern Australia: Electrophoretic, Morphological and Habitat Variation. Australian Journal of Zoology44:22358. Beatty, S.J., Morgan, D.L. and Gill, H.S. (2003). Reproductive biology of the large freshwater crayfish Cherax cainii in southwestern Australia. Marine & FreshwaterResearch54:597608. Beatty,S.J.,Morgan,D.L.andGill,H.S.(2004).Biologyofatranslocatedpopulation of the large freshwater crayfish, Cherax cainii (Austin & Ryan, 2002) in a WesternAustralianriver.Crustaceana77(11):13291351. Beatty,S.J.,Morgan,D.L.andGill,H.S.(2005).Lifehistoryandreproductivebiology of the gilgie Cherax quinquecarinatus, a freshwater crayfish endemic to south westernAustraliaJournalofCrustaceanBiology25(2):251262. Boulton,A.J.andHancock,P.J.(2006).Riversasgroundwaterdependentecosystems: a review of degrees of dependency, riverine processes and management implications.AustralianJournalofBotany54:133144. Centre of Excellence in Natural Resource Management (2005) Ecological water requirementsoftheBlackwoodRiverandtributariesNannuptoHutPool.Reportfor theWaterCorporationofWesternAustralia,February2005.,pg11 Crandall,K.A.,Fetzner,J.W.,Lawler,S.H.,Kinnersley,M.,andAustin,C.M.(1999). Phylogenetic relationships among the Australian and New Zealand genera of freshwater crayfishes (Decapoda : Parastacidae). Australian Journal of Zoology 47:199214. Freeze,R.A.andCherry,J.A.(1979).Groundwater.PrenticeHall,NewJersey. Gill, H.S., Hambleton, S.J., and Morgan, D.L. (1999). Is Gambusia holbrooki a major threattothenativefreshwaterfishesofsouthwesternAustralia?InSeret,B.& Sire, J.Y., (eds). Proceedings 5th IndoPacific Fish Conference (Noumea, 38 November1997).pp.7987.Paris:SocieteFrancaisedIchtyologie&Institutde RecherchepourleDevelopment. Gill, H.S., Renaud, C.B., Chapleau, F., Mayden, R.L., and Potter, I.C. (2003). Phylogeny of Living Parasitic Lampreys (Petromyzontiformes) Based on MorphologicalData.Copeia,2003(4):687703. Gill,H.S.,Wise,B.S.,Potter,I.C.andChaplin,J.A.(1996).Biannualspawningperiods and resultant divergent patterns of growth in the estuarine goby Pseudogobius olorum:temperatureinduced?MarineBiology125:453466. Hatton, T. and Evans, R. (1998). Dependence of ecosystems on groundwater and its significancetoAustralia.LandandWaterResourcesResearchandDevelopment Corporation,Canberra. Hayashi, M. and Rosenberry, D.O. (2002). Effects of ground water exchange on the hydrologyandecologyofsurfacewater.GroundWater40(3):309316. Humphreys,W.F.(2006).Aquifers:theultimategroundwaterdependentecosystems. AustralianJournalofBotany54:115132. 129
Horwitz,P.andAdams,M.(2000).Thesystematics,biogeographyandconservation status of species in the freshwater crayfish genus Engaewa Riek (Decapoda: Parastacidae)fromsouthwesternAustralia.InvertebrateTaxonomy14:655680. Morgan, D. and Beatty, S. (2004). Monitoring the Lions Weir Fishway Hotham River, Western Australia. Report to the Department of Environment, Government of WesternAustralia. Morgan, D.L., and Beatty, S.J. (2005). Baseline study on the fish and freshwater crayfish fauna in the Blackwood River and its tributaries receiving discharge fromtheYarragadeeAquifer.MurdochUniversity,WesternAustralia). Morgan, D.L. and Gill, H.S. (2000). Fish associations within the different inland habitats of lower southwestern Australia. Records of the Western Australian Museum20:3137. Morgan, D.L., Gill, H.S. and Potter, I.C. (1995). Life cycle, growth and diet of Balstons pygmy perch in its natural habitat of acidic pools. Journal of Fish Biology47:808825. Morgan, D. L., Gill, H. S., and Potter, I. C. (1998). Distribution, identification and biology of freshwaterfishesinsouthwestern Australia.Records of the Western AustralianMuseumSupplementNo.56.97pp. Morgan, D.L., Thorburn. D.C. and Gill, H.S. (2003). Salinization of southwestern Western Australian rivers and the implications for the inland fish fauna the BlackwoodRiver,acasestudy.PacificConservationBiology9:161171. Morgan,D.,Beatty,S.,Gill,H.,Thorburn,D.andRowland,A.(2004).Assessmentof groundwater discharge from the Yarragadee Aquifer on the fish and decapod fauna of RosaBrook.ReporttotheWaterCorporationofWesternAustralia. Morrissy, N. M. (1978). The past and present distribution of marron, Cherax tenuimanus,inWesternAustralia.FisheriesResearchBulletinofWesternAustralia 22:138. Murray,B.R.,Zeppel,M.J.B.,Hose,G.C.,Eamus,D.(2003).Groundwaterdependent ecosystems in Australia: its more than just water for rivers. Ecological Management&Restoration4:110113. Nickoll, R., and Horwitz, P. (2000). Evaluating flagship species for ecosystem restoration: a case study involving freshwater crayfish and a river in southwestern Australia. In Nature Conservation 5: Nature Conservation in ProductionEnvironments:ManagingtheMatrix.(EdsJ.I.Craig,N.Mitchell, andD.A.Saunders.)pp.55764.(SurreyBeattyandSons,2000.) Pen,L.J.andPotter,I.C.(1991)Reproduction,growthanddietofGambusiaholbrooki (Girard) in a temperate Australian river. Aquatic Conservation: Marine and FreshwaterEcosystems,1(2):159172. Pen,L.J.,Potter,I.C.andHilliard,R.W.(1991).BiologyofGalaxiellamundaMcDowall (Teleostei:Galaxiidae),includingacomparisonofthereproductivestrategiesof thisandthreeotherlocalspecies.JournalofFishBiology39:717731. Petts, G.E., Bickerton, M.A., Crawford, C., Lerner, D.N. and Evans, D. (1999). Flow management to sustain groundwaterdominated stream ecosystems. HydrologicalProcesses13:497513. 130
Potter, I.C. (1980). The Petromyzoniformes with particular reference to paired species.CanadianJournalofFisheriesandAquaticScience,37(11):15951615. Potter, I.C., Hilliard, R.W. and Bird, D.J. (1980). Metamorphosis in the southern hemispherelamprey,Geotriaaustralis.JournalofZoology,190(3):405430. Potter,I.C.andHilliard,R.W.(1987).Aproposalforthefunctionalandphylogenetic significance of differences in the dentition of lampreys (Agnatha: Petromyzontiformes).JournalofZoology.212(4):713737. Potter,I.C.Hilliard,R.W.andNeira,F.J.(1986).ThebiologyofAustralianlampreys. Deckker,Pde;Williams,WD(eds). Power,G.,Brown,R.S.andImhof,J.G.(1999).Groundwaterandfishinsightsfrom northernNorthAmerica.HydrologicalProcesses13:401422. Sear,D.A.,Armitage,P.D.andDawson,F.H.(1999).Groundwaterdominatedrivers. HydrologicalProcesses13:255276. SPSS(2005).StatisticalPackageVersion14.0forWindowsTM. Strategen (2006) South West Yarragadee Water Supply Development: Sustainability Evaluation/Environmental Review & Management Programme Volume 2. ReportfortheWaterCorporation,February2006.
131
APPENDIX1: Densities of fish and freshwater crayfish at main channel sites of the Blackwood River (see Methodssectionforsamplingprotocols).
Denny Road near Rosa Brook confluence Site Total Mean species density m2 (total number captured) in the Blackwood River using seine nets and/or electrofishing area sampled (m2) Native fishes Feral fishes Decapod crustaceans
Galaxias occidentalis Edelia vittata Afurcagobius suppositus Tandanus bostocki Leptatherina wallacei Gambusia holbrooki Oncorhynchus mykiss Cherax cainii Cherax quinquecarinatus Cherax preisii Cherax crassimanus Palaemonetes australis
Spring 2005 Summer 2006 Autumn 2006 Winter 2006 Spring 2006 Total
190 120 117.5 185 150 762.5 0.421 (26) 0.173 (32) 0.347 (52) 0.144 (110)
0.039 (7) 0.050 (6) 0.190 (31) 0.430 (8) 0.047 (7) 0.070 (53)
0.005 (1)
0.001 (1)
0.008 (6)
0.018 (4) 0.089 (13) 0.992 (61) 0.227 (42) 0.733 (110) 0.300 (229)
1.444 (150) 0.519 (96) 0.040 (6)
0.006 (1) 0.067 (11) 0.046 (3)
0.172 (23) 0.014 (1)
0.331 (252)
0.197 (15)
0.032 (24)
4.418 (785) 3.000 (390) 5.370 (500) 2.168 (401) 1.067 (160) 2.932 (2236)
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Milyeannup Pool Site Total Mean species density m2 (total number captured) in the Blackwood River using seine nets and/or electrofishing area sampled (m2) Native fishes Feral fishes Decapod crustaceans
Galaxias occidentalis Edelia vittata Afurcagobius suppositus Pseudogobius olorum Leptatherina wallacei Gambusia holbrooki Oncorhynchus mykiss Cherax cainii Cherax quinquecarinatus Cherax preisii Cherax crassimanus Palaemonetes australis
Summer 2006 Winter 2006 Spring 2006 Total
250 210 73 533
0.004 (1) 0.157 (33)
0.005 (1)
0.096 (24) 0.005 (1)
0.032 (8)
0.064 (34)
0.002 (1)
0.047 (25)
0.015 (8)
0.204 (51) 0.476 (100) 0.247 (18) 0.317 (169)
0.004 (5)
0.004 (1)
0.004 (1) 0.204 (51) 1.190 (250) 0.014 (12)
0.009 (5)
0.002 (1)
0.002 (1)
0.587 (313)
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Jalbarragup Rd crossing Site Total Mean species density m2 (total number captured) in the Blackwood River using seine nets and/or electrofishing area sampled (m2) Native fishes Feral fishes Decapod crustaceans
Spring 2005 Summer 2006 Autumn 2006 Winter 2006 Spring 2006 Total
146 78 180 330 110 844
0.212 (31) 0.247 (64) 0.072 (13) 0.030 (10) 0 0.140 (118)
0.274 (40) 0.007 (2) 0.017 (3) 0.011 (2) 0.197 (13) 0.071 (60)
0.096 (14) 0.461 (36)
0.103 (34) 0.073 (8) 0.109 (92)
2.692 (393) 0.262 (67) 1.694 (325) 0.027 (9) 0.833 (120) 1.083 (914)
0.082 (12) 1.167 (91) 0.75 (135)
0.158 (23) 0.013 (1)
0.007 (1)
6.918 (1010)
0.268 (226)
0.014 (12)
0.027 (23)
0.001 (1)
0.001 (1)
0.139 (20) 1.515 (500) 0.509 (56) 1.789 (1586)
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Quigup Site Total Mean species density m2 (total number captured) in the Blackwood River using seine nets and/or electrofishing area sampled (m2) Native fishes Feral fishes Decapod crustaceans
Spring 2005 Summer 2006 Autumn 2006 Winter 2006 Total
85 444 180 90 799
0.270 (23) 0.124 (55) 0.044 (8)
0.141 (12) 0.002 (1) 0.167 (3) 0.056 (10) 0.011 (1) 0.030 (24)
0.318 (27) 0.036 (16)
0.012 (86)
0.004 (3)
0.044 (4) 0.059 (47)
0.612 (52) 0.365 (126) 1.728 (311) 0.378 (34) 0.655 (523)
0.012 (1)
0.012 (1) 0.022 (10)
1.444 (260)
0.033 (6)
0.006 (1)
0.325 (260)
0.009 (7)
0.001 (1)
0.001 (1)
0.012 (10)
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APPENDIX2: Densities of fish and freshwater crayfish at tributary sites of the Blackwood River (see Methods sectionforsamplingprotocols).
Poison Gully Season Total Mean species density m2 (total number captured) using seine nets and/or electrofishing. area sampled Native fishes Feral fishes Freshwater crayfishes 2 (m )
Nannatherina balstoni Galaxias occidentalis Edelia vittata Bostockia porosa Galaxiella munda Afurcagobius suppositus Gambusia holbrooki Oncorhynchus mykiss Cherax cainii Cherax quinquecarinatus Cherax preisii Cherax crassimanus
Spring 2005 Summer 2006 Autumn 2006 Winter 2006 Total
90 90 40 20 240
0.033 (4) 0.042 (2) 0.05 (19) 1.33 (20) 0.520 (45)
0.008 (1)
0.012 (2) 0.03 (2)
0.008 (1) 0.008 (1)
0.017 (2)
0.344 (31) 0.733 (56)
0.081 (8)
0.045 (2) 0.067 (1) 0.033 (5) 0.6 (12) 0.390 (104)
0.015 (3)
0.002 (2)
0.005 (2)
0.009 (3)
0.022 (8)
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Layman Brook Season Total Mean species density m2 (total number captured) using seine nets and/or electrofishing. area sampled Native fishes Feral fishes Freshwater crayfishes (m2)
Spring 2005 Summer 2006 Total
300 10.5 310.5
0.081 (13)
0.027 (13)
0.11 (33) 0.136 (1) 0.139 (34)
137
Rosa Brook Season Total Mean species density m2 (total number captured) using seine and/or electrofishing. area sampled Native Fishes Feral Fishes Freshwater Crayfish (m2)
Spring 2005 Summer 2006 Total
350 200 550
0.311 (95)
0.023 (8)
0.024 (8)
0.033 (1)
0.116 (95)
0.012 (8)
0.012 (8)
0.002 (1)
0.071 (24) 0.577 (110) 0.324 (134)
138
McAtee Brook Season/Site Total Mean species density m2 (total number captured) using seine nets and/or electrofishing. area sampled Native fishes Feral fishes Freshwater crayfishes (m2)
Crouch Road Spring 2005 Summer 2006 Autumn 2006 Total
550 570 75 1195
0.024 (18) 0.056 (32)
0.042 (50)
0.035 (19) 0.167 (98) 0.067 (8) 0.105 (125)
0.016 (6) 0.008 (6) 0.025 (4) 0.014 (16)
0.005 (1) 0.017 (1) 0.002 (2)
0.008 (7)
0.053 (25)
0.006 (7)
0.021 (25)
0.033 (19) 0.140 (88) 0.400 (32) 0.116 (139)
0.001 (1)
0.010 (7)
0.001 (1)
0.072 (5) 0.010 (12)
Longbottom Road Spring 2005 Summer 2006 Total
120 65 185 0.015 (1) 0.005 (1)
0.308 (32) 0.154 (10) 0.227 (42)
0.022 (3) 0.015 (1) 0.005 (1)
0.016 (3)
0.171 (21) 0.108 (7) 0.0151 (28)
139
Section 2
Crayfish burrowing activity in the region of the Yarragadee Discharge Zone, Blackwood River
AKoenders&PHJHorwitz
140
AIMSANDOBJECTIVES
The overall study aimed to develop an understanding of how fish and freshwater crayfishutilisetheBlackwoodRiverandtributariesthroughouttheseasons,andhow this movement may be related to changes in flow, groundwater discharge, and/or waterphysicochemistry.Informationonflowsandwaterphysicochemistryhasbeen gathered with the aim of linking changes in these attributes to patterns of fauna movements.Thestudyspecificallyexaminesthesignificanceoftheyearroundinput of fresh groundwater baseflow from the Yarragadee Aquifer to the fauna. The findings will assist the Department of Environment in identifying key parts of the river system being utilised by the endemic fauna and in characterising critical componentsorattributesofthewaterregimethatarerequiredtomaintainthem. Within this overall project, an investigation of the freshwater crayfish burrowing activitywasconductedto: a) determinetheseasonalchangestoburrowingactivityforeachspeciesateach sitechosen,andrelatethistogroundwater/surfacewaterchanges;and b) relate these changes to the occurrence of different species in surface waters overthedurationoftheinvestigation. Thesefieldinvestigationsenabledustomakelimitedpredictionsabouttheeffectsof groundwaterchangesonfreshwatercrayfishdistributionandabundanceinthearea ofinterest. A separate preliminary investigation sought to determine whether the Yarragadee dischargeinthestudyareacouldbechemicallycharacterised(andthereforewhether fishorcrayfishspeciesmightbeabletodetectitspresenceaspartoftheirmigratory orhomingbehaviour). Thisreportprovides: a) results for both the burrowing activity and the water physicochemistry componentsofthestudy; b) a discussion of the methods used to examine the relationships between burrowing freshwater crayfish and ground and surface water level changes; and c) aseriesofsuggestionsandrecommendationsforareasofworkrequiredfora successful determination of critical questions that preliminary investigations raise.
141
CRAYFISHBURROWING METHODS
Transectestablishmentanddesign
Transect sites were selected to provide some comparative information about treatment systems receiving a prominent discharge from the Yarragadee aquifer (Milyeannup Brook and Poison Gully) and those not receiving such a discharge (Layman Brook, Rosa Brook and McAtee Brook). Important flowing water geomorphological habitats to be compared are headwaters, gullies (more deeply incised)andswampgulliesandtributariesofthestreams(Table1,withfulldetailsof transects in Appendix A). It was considered essential to gather faunal and water parameterdatainthiscontext,andfromafullseasonalperspective.
Table1Transectcomparisons.
Typeofsite Headwater Gully Gully(swamp) Westernflowing tributary Easternflowing tributary
Treatmenttransect MilyeannupBrook,MB2 PoisonGully,PG1 MilyeannupBrook,MB4
Controltransect RosaBrook,RB3a LaymanBrook,LB2 RosaBrook,RB2a McAteeBrook,MC2a LaymanBrook,LB1a RosaBrook,RB3b RosaBrook,RB2b
McAteeBrook,MC2b LaymanBrook,LB1b (MilyeannupBrook,MB4) RosaBrook,RB3b
Transects were marked at one end with a star picket on the left bank facing downstreamandattheotherendwithapiezometerontheoppositebank.Transects havebeenmappedandarebetween13and70minlength,dependingontheterrain. From2to5quadratsweremappedalongeachtransect,againdependingonterrain andtransectlength.
Watercharacteristics
Ateachtransect,surfacewaterdepth(andgroundwaterdepthwherepossible)were measured and temperature, pH and conductivity of each recorded (using portable calibrated WTW water meters). A 500 mL sample of surface water and, where possible purged groundwater, were collected from each transect. Water samples werekeptoniceuntiltakentothelabwheretheywerestoredat20oCuntilanalysis. 142
In addition, 50 mL of water was filtered using a Whatman glass fibre filter (45 nm filter pore size) in a filter attachment to a syringe and acidified with 1 mL of 14 M nitric acid. All containers and other items used to handle water samples had been acidrinsedwith1%HCl.
A.
B.
C.
D.
E.
F.
Figure1Examplesoftransectdetails. A.Piezometer,LaymanBrookdownstreamtributary;B.MeasurementofwaterlevelatRosa Brook,MowenRoad;C.Extendingmeasuringtapealongtransectfromstaketopiezometer, downstream tributary of Layman Brook; D. Measuring water parameters at St Patricks Elbow on Blackwood River; E. Artificial burrows at Poison Gully downstream site; F. SearchingforburrowsatRosaBrook,MowenRoad.
143
Crayfishburrowmonitoring
Estimationofburrowdensities Burrow densities are calculated for the number of burrows per metre of transect. CountingofburrowsduringOctobertoDecember2005wasundertakenforupto5 sectionsofeachtransect.Eachsectionwasapproximately1minlength,spacedalong the transect in burrow hotspots, and the number of burrows counted where they occurred within a metre of the transect line. This method was amended in January 2006 and thereafter to count burrows along the full length of each transect. As burrows are distributed in clumps, burrow densities between the two collection periodsarenotequivalentandsomecorrectionwasneeded. The most comprehensive data available are for MB4, so this transect was used to obtainacorrectionfactorthatwasthenappliedtoalltransects. BurrowdensitywascalculatedforDecember2005,thetimewhenwaterlevelswere low and the greatest number of burrows was visible, using the total length of all quadratssearched.Thisvaluewas4.46burrows/m.BurrowdensityforJanuary2006 wasobtainedbyusingthetotallengthofthetransectandwas0.53burrows/m.This indicatesthatburrowdensityusingquadratsearchingisoverestimatedbyafactorof 8.4 (4.46/0.53). Therefore, burrow densities from October to December 2005 were corrected by dividing by 8.4 forall transects. The only transects for which this was not done were those that went across deep gullies, where the quadrats coincided withthefunctionaltransect,i.e.MB2,RB2aandRB3a. Burrowclassification Burrows were classified by habitat according to Horwitz and Richardson (1986)1. Note that this scheme is dependent on water level. As water levels changed dramatically in many transects, the habitat type of most burrows depended on the season. In addition to burrowing habitat type, indirect evidence of burrowing activity was recordedforeachburrowas oneof threecharacter states:open,soilpelletsor plug (seeFigure2).Someburrowssimplyopenedasanentranceholeintheground.Fresh soil pellets around a burrow entrance were interpreted as evidence of recent burrowingactivity.Burrowswiththeirentrancecompletelyblockedwithasoilplug werealsoobserved,andtakentobeevidenceofcompleteclosureofaburrowsystem to retain moisture during drier seasons. A qualitative appraisal of soil type was recorded.
Horwitz PHJ & Richardson AMM. 1986. An ecological classification of the burrows of Australian freshwater crayfish. Aust. J. Mar. Freshw. Res. 37, 237-242. 144
Table2Crayfishburrowtypes.FromHorwitzandRichardson(1986).
Burrow type 1a 1b 2
Locationinhabitat Permanentwater Connectedto permanentwater Connectedtowater table
Watersource Permanentwaterbody Groundwater&surface waterrunoff
Hydrological zone Phreatic Epiphreatic
Observationofcrayfishattransects Observations of crayfish at transects were carried out during the day and by spotlighting and trapping after dark. In addition, some crayfish burrows were excavated near each transect, without disturbing burrows along transects. Where possible,crayfishwereidentifiedinthefield.Somecrayfishwerepreservedin75% ethanolandkeptoniceandlaterstoredat4oCforidentificationandDNAanalysisin anysubsequentwork.
A.
B.
C.
Figure2
D.
Examples of burrow types (adapted from Horwitz and Richardson, 1986) and burrowing activity. A. Type 1a burrow opening below water level (Rosa Brook, Mowen Rd site); B. Type 1b burrow opening at water level (Milyeannup Brook, MilyeannupRdsite);C.Type2burrowsopeningabovewaterlevelbutexpectedtobe connected to the water table, pencil points to plugged burrow, arrow points to burrowwithpelletsindicatingrecentburrowingactivity;D.Bankwithahighdegree ofrecentburrowingactivity(C.,D.tributaryofMcAteeBrook,CrouchRdsite).
145
RESULTS
Datacollectedforeachtransectispresentedinthefollowingformat: a) Transectnameandsitecode b) Transectcharacteristics c) Speciesobserved d) BurrowdensitiesfortheperiodofOctober2005September2006 e) Periodsinwhichsurfacewaterispresent f) GroundwaterlevelsbetweenSeptember2005andSeptember20062. Comments are then made summarising the data for each transect: surface water characteristics, groundwater conditions, and seasonal burrowing habitats and activities.(FullwaterchemistrydataarepresentedinAppendixB,andinformation onspeciescollectedinAppendixC.) Thisisfollowedbycomparisonsbetweensites.
TransectData
BlackwoodRiver,StPatricksElbow DennyRd,BW4 Transectcharacteristics The transect stretched across a backflow floodplain into the middle of the main channel of the River. No burrows were observed along the transect; although numerousburrowsoccurredonthebanksofthemainchannel. Blackwood River St Patrick's Elbow BW4 0.0 -0.2 -0.4 -0.6 -0.8 -1.0 -1.2 -1.4 Dry -1.6 Sep 05 Oct 05 Nov 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
Figure3 GroundwaterdepthsatBlackwoodRivertransectmeasuredinthepiezometer. Surfacewaterwaspresentthroughoutinthemainchanneloftheriver.
Groundwater depth (m)

All figures showing groundwater depths stop at the maximum depth of the piezometer, so this underestimates the groundwater fluctuations over the year.
2
146
Summary ThefloodplainareawaswaterloggedatleastuntilNovember2005.ByJanuary2006 the surface water on the floodplain had disappeared completely and groundwater depth was greater than 1.6 m at the piezometer. Conductivity of the main channel and groundwater at this site were the highest measured in the study, and in both peakedaround7700S/cminAugustSeptember2006. Nocrayfishorburrowswereobservedinthefloodplainpartofthistransect.Crayfish were collected from the main channel (C. quinquecarinatus) and open burrows were observedinthebankoneachvisit,butnoburrowdensitieswererecorded. LaymanBrookGully LaymanRoad,LB1a Transectcharacteristics Thecreekproperisupto4mwidewithclearwater.Thetransectwasplacedalong thecreekbedfor50m.Ononesideisasteepforestedslope,thecreekbedandbanks areveryrocky(laterite).
Layman Brook Denny Road LB1a
Species observed:
0.25 Type 1a Type 1b Type 2
Gilgie - C. quinquecarinatus
B u rro w d e n s itie s (n u m b e r/m )
0.20
0.15
0.10
0.05
0.00 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06
Figure4
SeasonalproportionsofburrowtypesforLB1a.
147
Layman Brook Denny Rd LB1a

Surface water present 0.0
-0.1
-0.2
-0.3
-0.4
-0.5
-0.6
Dry
Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
Figure5
Seasonalchangesingroundwaterdepth.Thepiezometerwentdowntobedrockin yellowsandyclay.
Summary ThepiezometerwasdrybyDecember2005(sogroundwaterlevelswerebelow0.6m after this time until August 2006). Note that the piezometer was dry in September 2006;demonstratingthedryautumnandwinterexperiencedin2006. Conductivityandtemperatureofsurfacewaterincreasedinsummer,aswaterlevel dropped. Surface waters were slightly turbid and flowing, making visibility of burrows difficult during wetter sampling occasions (underestimating burrow density). AllburrowsareassumedtobethoseofC.quinquecarinatus,theonlyspeciesfoundin theLaymanBrooksystem(seealsosection1).Burrowdensityisrelativelylow;only openburrowsfound(noburrowingactivityobserved,mostlikelybecausetherocky substrateprovideslittleopportunityforburrowing).Notetheshifttotype2burrows intheabsenceofsurfacewater. LaymanBrookWesternFlowingTributary LaymanRd,LB1b Transectcharacteristics ThistransectisonatributaryofLaymanBrook(infactitisthetributarydischarging intotheBrookimmediatelyupstreamofLB1a)andrunsalongthecreekbedfor45m. Creekisupto2mwidewithclearwaterandarocky(laterite)bed.Itissituatedin relativelyopenforestonshallowlateriticsoil.
148
Layman Brook Denny Road LB1b

Speciesobserved:
GilgieC.quinquecarinatus
0.3
0.2
0.1
0.0 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
Figure6 Burrowtypes.
Summary Similar characteristics to main channel at LB1a. Conductivity and temperature of surfacewaterincreasedinsummer,aswaterleveldropped.Conductivityofsurface water peaked at 500 S/cm in January 2006. Groundwater depth was greater than 0.65 m at the piezometer at all months except August 2006, even though surface waterswerepresent.Theseobservationsallsuggestthatthetributaryreceivesrunoff, notgroundwaterdischarge. Burrowdensityishigherthaninthemainchannel,possiblyduetoagreateramount ofclay/loamincreekbed.Overallobservableburrowdensitywashighestwhenthe creek was dry, with a shift to type 2 burrows. In summer, all burrows were above water level, however, no burrowing activity was observed (only open burrows found). LaymanBrookHeadwater CrouchRd,LB2 Transectcharacteristics Transect (50 m) runs in gully along shallow, 1 m wide creek with clear water and sandypatchesinterspersedwithrockyareas(laterite).Creekinforestedarea.
Burrow density (number/m)
149
Layman Brook Crouch Road LB2

0.8 Type 1a Type 1b Type 2 0.6
Speciesobserved:
0.4
0.2
Figure7
BurrowdensitiesforLB2.Noburrowingactivityobserved.
Layman Brook Crouch Rd LB2

-0.1
Groundwater depth (m) Dry
-0.2
-0.3
-0.4
-0.5
-0.6 Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
Figure8
GroundwaterdepthatLB2.Piezometerdowntogravellyclay.
Summary ThesurfacewaterdisappearedafterDecember2005andreappearedinAugust2006. Surface water was characterised by low conductivity which remained low at all times, peaking at 250 S/cm in September 2006. Groundwater showed relatively constant levels except for the dry periods between March and July 2006, consistent withthepresenceorabsenceofsurfacewater. Burrow densitieswere intermediate, withall burrowsout of waterin summer, and alltotallysubmergedwhensurfacewaterispresent,suggestingsimplyconstructed
150
burrows without multiple openings. No burrowing activity was observed whilst surfacewaterreceded. MilyeannupBrookGully HelyarRd,MB2 Transectcharacteristics This short transect (7.5 m) runs across a deeply incised creek gully. Creek is permanentlyflowing,deeperinwinterwithconstantshallowflowinsummer.Creek banksandbedaremostlyclay(greysandyclayoverbrownclayeysand)withmany burrowsinthem.Thecreekiscrossedbyfallenlogsandrunsthroughforest. Millyeannup Brook Helyar Road MB2 Speciesobserved:
10 Type 1a Type 1b Type 2
GilgieC.quinquecarinatus MarronC.cainii RestrictedGilgieC.crassimanus
0 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
Figure9
BurrowdensitiesforMB2.Noburrowingactivityobserved.
Summary Surfacewaterconductivitywasrelativelylow,butincreasinginsummer(270490 S/cm),althoughwatertemperaturesremainedlow(below18oC). Very high burrow density (as holes in the bank) were recorded during drier times, with more burrow openings visible at low water levels, probably seriously overestimating the number of crayfish at the site, and the amount of burrowing, ratherthanrecordingshallowburrowsusedbyshelteringcrayfishinpastyears.This site had high crayfish diversity; although only open burrows were recorded (no burrowingactivitywasseen).Steepsidedbanks,undercutinplaces,permanentfresh clearandcoolwater,thepresenceofcoarsewoodydebrisandrocksallcontributed tohighlevelsofhabitatdiversityinthecreek,capableofsupportingthreespeciesof freshwatercrayfish(Figure9),althoughinsection1,Koonacswerealsorecordedin thisBrook. Nopiezometerdatawereavailableforthissite. 151
MilyeannupBrookWesterntributary
MilyeannupRd,MB4
Transectcharacteristics Long (70 m) meandering transect positioned at the margin of an extensive swamp systemthatformstheheadwaterregionofMilyeannupBrook.Transectwithsandy clayeysoil,crossingseveralephemeralpools.Wooded,denseshrubbyvegetation. Milyeannup Brook swamp MB4 Surface water present Speciesobserved:
40 Pellets Plug 30
Burrowing activity (% total burrows)
GilgieC.quinquecarinatus RestrictedGilgieC.crassimanus KoonacC.preissii
20
10
0 Oct 05 Nov 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
Figure10
BurrowingactivityforMB4.Asthissitewasdryformostofthestudyperiod,all burrowswereoftype2.
Milyeannup Brook upstream swamp MB4

-0.2
-0.4
-0.6
-0.8
-1.0
-1.2
Dry
Sep 05 Oct 05 Nov 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
Figure11
GroundwaterdepthsforMB4.Piezometerinsandyclayeysoil.
Summary Water conductivity was low (groundwater up to 400 S/cm, surface waters lower thanthis).SurfacewaterswerepresentonlyuptoOctober2005(didnotreappearin the 2006 wet season). Groundwater levels remained very low between March and July2006atleast,butcameveryclosetothesurfacebySeptember2006. 152
This site had intermediate burrow density (0.53 burrows/m). Instead of showing burrow densities, Figure 10 shows the proportion of burrow openings with burrowingactivityoveraseasonalannualsequence.Freshpelletssignifyburrowing activity,andthemostintensiveburrowbuilding/cleaningperiodoccursimmediately priortosurfacewaterdryingup,andduringthegroundwaterdeclinephase.Some burrowing occurred activity again in September 2006 when the surface sediments were saturated. Species diversity was high, and this was the only site where a Koonacwasfound.Furtherworkisrequiredtodeterminewhichspecieshavebeen burrowing,andwhetherhabitatpartitioningisevident McAteeBrookGullyControl CrouchRd,MC2a Transectcharacteristics: Controlgullysitewithtransect(60m)acrosscreek.Transectincorporatessmalleast flowingtributary,maincreekchannelandside(overflow)channelinthefloodplain areaofthecreek.Creekbediswidewithflowingwater.Mainchannelwithexposed lateriticbedrock. McAtee Brook Crouch Road MC2a Speciesobserved:
0.7 Type 1a Type 1b Type 2 0.6
GilgieC.quinquecarinatus MarronC.cainii RestrictedGilgieC.crassimanus
0.5
0.4
0.3
0.2
0.1
Figure12
BurrowdensitiesforMC2a.Littleburrowingactivityobserved,withonlyoneburrow pluggedinDecember05.
153
McAtee Brook Crouch Rd MC2a

-0.1
Groundwater depth (m) Dry
-0.2
-0.3
-0.4
-0.5 Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
Figure13
GroundwaterdepthsatMC2a.
Summary Conductivity was low in winter and peaked in summer (210 1230 S/cm). Creek waterflowedallyear,slowingtoveryslighttrickleattheheight ofthedry season. Surfacewaterwasslightlyturbidallyear,clearestatwettesttime,mostturbidwith iron staining in drier times. Side tributary flowed in September and October 2005 (runoff) but very little evidence of crayfish was found in this habitat. Back channel hadstagnant,ironstainedwaterforthewetterpartoftheyearonly. GroundwaterlevelsdeclinedafterSeptember2005andthepiezometer(placedinthe floodplain) remained dry (<0.5m) for at least 9 months, even though surface water waspresentinthecreek,suggestingsomegroundwaterdischargeintothesystem. Intermediate burrow density was found mostly in side channel and on the creek bank, with the habitat diversity (permanent water, rocky substrate with deeper pools, deeper loamy soils in the floodplain) supporting three crayfish species. All threeburrowhabitatsarepresentallyearround. McAteeBrookWesterntributarycontrol CrouchRd,MC2b Transectcharacteristics ThistransectisonatributaryofMcAteeBrooknear(enteringdownstreamof)MC2a. Itrunsalongthecreekbedfor40m.Thecreekisupto2mwidewithclearwater overlateriticsoil.Burrowswereconcentratedinsiltandloamofthebankandcreek bedalongasharpbend.
154
McAtee Brook tributary Crouch Road MC2b

Speciesobserved:
3.0
2.5
2.0
1.5
1.0
0.5
Burrowing activity MC2b

30 Plug Pellets
25
20
15
10
0 Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06
Figure14 Burrowdensities(top)andburrowingactivity(bottom)forMC2b.
155
McAtee Brook Tributary Crouch Rd MC2b

-0.2
-0.4
-0.6
-0.8
-1.0
Dry
Figure15
GroundwaterdepthsforMC2b.
Summary Surface water was clear and stained, had low conductivity (240520 S/cm), and occurred in October 2005, and again in August and September 2006 responding to runoffonly. Groundwater levels in the piezometer dropped markedly between October and December 2005, the period in which most burrowing activity occurred. Subsequent activitylevelsinJanuary,MarchandJulyarelikelytoberepeatmeasuresofthesame burrowssystemsindriertimes. This tributary had high burrow density, and high burrowing activity levels (all attributable to the species C. quinquecarinatus) as groundwater levels dropped and surface water disappeared. After burrows reopened in winter/spring, a great number ofjuvenileGilgieswereobservedintheleaf litteronthecreekbed, butno mature individuals were located. These observations and recordings are together consistent with the idea that mature Gilgies migrate up the tributary to breed and burrowinforsummer,andmoveintodownstreamintothemainchannelagainupon emergence,leavingthetributaryasanurseryfor0+classes. PoisonGullyGully(swamp) BlackwoodRd,PG1 Transectcharacteristics Twotransectswereplaced.Thefirstranacrossandperpendiculartothecreekfora distance of 40 m. Later a second transect was placed alongside the creek for 20 m, entirelyintheorganicsoil.Piezometerwasplacedupslope,insandysoil. 156
Poison Gully Blackwood Rd PG1

Speciesobserved:
GilgieC.quinquecarinatus RestrictedGilgieC.crassimanus MarronC.cainii
-0.2
-0.4
-0.6
-0.8
-1.0
Dry
Sep 05 Oct 05 Nov 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
Figure16
GroundwaterdepthforPG1.
Summary Thecreekrunsthroughaheathylongitudinalswampsystemwithorganicsoilupto 0.5m depth in places, in the lowest part of the swamp. The organic soil becomes shallowerawayfromthecreek,upslope.Elsewhereandunderlyingtheorganicsoils aresandysoils.Waterinthecreekwasveryclearandunstainedflowingwater,ina channelupto1mwidewithpeatbanks(stabilisedbyrootsofheathspecies).Inthe channel was unconsolidated organic sediment. There were several peat clumps isolatedinthecreekchannel. Water conductivity (< 290 S/cm) and pH (4.65.5) were both comparatively very low.Streamcontinuedtoflowallyearround. No burrows were observed on the perpendicular transect. Burrow density for the second transect was relatively low, although crayfish diversity was high. Crayfish wereobservedtodisappearintotheunconsolidatedsedimentwhendisturbed.Loose poorly defined burrows were discerned in the banks of the creek and underneath peatclumps. RosaBrookGullyControl CrouchRd,RB2a Transectcharacteristics Transectliesacrossdeepcreekgully(8.3m).Creekbanksandbedwithclaysubstrate andalotofburrows.Piezometerplacedonalowbankabovethegully.
157
Rosa Brook Crouch Road RB2a

14 Type 1a Type 1b Type 2
Speciesobserved:
12
10
Figure17
BurrowdensitiesforRB2a.Onlyopenburrows recorded;noburrowingactivityobserved.

Rosa Brook Crouch Rd RB2a
Surface water present 0.0 -0.2 -0.4 -0.6 -0.8 -1.0 -1.2 -1.4
Dry
Figure18
GroundwaterdepthsforRB2a
Summary Surface water dried in January 2006 and only reappeared in September 2006. All surface waters were relatively fresh (360450 S/cm). Surface water presence and groundwater levels are, in the main, consistent with one another, and exemplify a zone in the creek system where groundwater recharge occurs; despite reaches upstreamhavingpermanentwater,middlereachesdryoutinsummer.
158
Although burrow density was extremelyhigh, all burrows were open only, and no burrowingactivity(pelletsorplugs) was observed aswater level receded.Crayfish wereobservedinburrowsandonthesurface. RosaBrookWesternTributaryControl CrouchRd,RB2b Transectcharacteristics Transect liesalongcreekbedfor50m.Creek is upto 1.5m wide withclearwater. Creekbedhassilt,clayandrockypatches.Therearesteepbanksbothsidesinseveral places.Edgesareforested.Piezometerdowntogravelyclay. Rosa Brook tributary RB2b Speciesobserved:
2.5
2.0
1.5
1.0
0.5
Rosa Brook tributary Crouch Road RB2b

Surface water present
25 Pellets Plug
20
15
10
Figure19 Burrowdensities(top),burrowingactivity(below).
159
Rosa Brook Tributary Crouch Rd RB2b

-0.2
-0.4
-0.6
-0.8
-1.0
-1.2
Dry-1.4
Summary Surface water presence and groundwater level changes are consistent with one another(asperRB2a).Waterconductivitywaslow(230280S/cm).Thistransecthad highburrowingdensities,andburrowingactivitycoincidedwithdecreaseinsurface waterlevel.SimilarlytoMC2b,manyjuvenilecrayfishwereobservedintheleaflitter whensurfacewatersreturnedinautumn. RosaBrookHeadwaterControl MowenRd,RB3a Transectcharacteristics Transect cuts across gully (6 m). Creek has turbid flowing water, with soft silty banks.Forestedoneasternside,sedgeswamponwesternside(RB3b). Speciesobserved Nonecollectedfromtransect;GilgiesC.quinquecarinatusfoundinfiredamnextto brook. Summary Asthecreekheldwaterthroughoutsummer,crayfishhadamplerefugewithasteep undercut, permanent water, and coarse woody debris in the creek. Conductivity of thesurfacewaterwasintermediate(350670S/cm). Intermediateburrowdensityrecorded(between2and2.5burrows/mtransect)when surfacewaterlevelsinthecreekdropped,exposingtheburrowsinthesteepbanks. Onlyopenburrowsobserved,noburrowingactivitynoted,andahighproportionof burrowsweretype1b,withopeningsaboveandbelowsurfacewater.
Sep 05
Oct 05
Dec 05
Jan 06
Mar 06
Jul 06
Aug 06 Sep 06
160
RosaBrookGully(swamp)
MowenRd,RB3b
Transectcharacteristics The transect (43 m) lies across a sloping densely vegetated sedge seepage swamp draining into the Rosa Brook at RB3b. Several small shallow permanently trickling creekscrossthetransect.SometimebetweentheJulyandAugusttrips,theareawas subjecttoacontrolledburn. Rosa Brook swamp Mowen Road RB2b Speciesobserved:
0.6
0.4
0.2
Figure22
BurrowdensitiesforRB3b.
Rosa Brook Mowen Rd RB3

-0.2
-0.4
-0.6
-0.8
Sep 05 Oct 05 Dec 05 Jan 06 Mar 06
Jul 06
Aug 06 Sep 06
Figure23
GroundwaterdepthforRB3aandRB3b.
Summary Surface water was present throughout summer in the form of shallow seepage trickles.Burrowdensityisquitehigh,with someburrowingactivityobserved.This sitehasburrowsthatarepotentiallyinhabitedbyEngaewasp.butthishasnotbeen verifiedtodate.
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Transectcomparisons Headwaters: While both headwater sites received surface water runoff seasonally (September to December), conditions in Layman Brook with runoff only3 were different to Rosa Brook which cuts into (and therefore receives discharge from) the Leederville Aquifer; the catchment sizes differ, with Layman Brook being smaller than Rosa Brook and the channel only capable of delivering a smaller flow. Only Gilgieswereobservedinbothcreeks(Table3),althoughthehabitatdiversityatRosa Brooksuggeststhatotherspeciesarelikelytobepresent.
Table3 Headwatercreekcomparisons.
Transect
Creeksubstrate BurrowDensity (no./m) Speciespresent Surfacewater
LaymanBrook CrouchRd LB2 Whiteclayeysandwith lateriteoutcrops 0.7 Gilgie(C.quinquecarinatus) Clear DryinMarch06
RosaBrook MowenRd RB3a Lightbrownloam 2.4 Gilgie(C.quinquecarinatus) Turbid Surfacewaterpresentall year 347674
Conductivity( S/cm) 192256 Gullies:ThedeepcreekgullyatMilyeannupBrookwasfedbyYarragadeedischarge pluscatchmentrunoff.LaymanBrook,RosaBrook(West)andMcAteeBrook(East) appearnottoreceiveinputfromtheYarragadeeAquifer(Table4).Milyeannupand McAtee Brooks had the highest species diversity, including the restricted Gilgie. In addition, Milyeannup Brook had the highest burrow density and low water conductivities.LaymanBrookalsoexperienceslowwaterconductivitiesuntilitdries completelyinautumn,buttheseareprobablymoreindicativeofsurfacerunoffand shallowlateriticsoils.WaterconductivityinMcAteeBrookwashighlyseasonalbut the permanent flows and iron staining throughout the year suggest some groundwaterdischarge,probablyfromtheLeedervilleaquifer.
Only the effects of runoff were detected in the Layman Brook headwater site; no evidence of groundwater discharge was observed in transects.
3
162
Table4
Gullycomparisons.
Transect
Layman Bk Crouch Rd LB1a

Rocky laterite 0.2 Gilgie Clear Present 237-508
Milyeannup Bk Helyar Rd MB2

Clay with many snags 8.0 Gilgie, Marron, restricted Gilgie Clear Present 272-490
Rosa Bk Crouch Rd RB3a

Mud 2.4 Gilgie Muddy Present 347-674
McAtee Bk Crouch Rd MC2a

Large rocks Much iron 0.5 Gilgie, Marron, restricted Gilgie Clear Present 210-1230
Creek substrate Burrow density (no./m) Species diversity Surface water Conductivity (S/cm)
Swampgullies:Threeswampgullytransectsweresetup:PoisonGully(yearround input from the Yarragadee Aquifer), Milyeannup Brook (within discharge zone but upstream of permanent Yarragadee discharge) and Rosa Brook (no input from Yarragadee)(Table5).AllthreesitesarecharacterisedbylowconductivityandpHof groundwater,butthesitesatPoisonGullyandMilyeannupBrookhavelowervalues than Rosa Brook and in contrast to Rosa Brook, little or no iron staining. Burrow densitywashighestforRosaBrook;thisareaisextremelydenselyvegetatedwitha soft, permanently wet substrate and therefore provides burrowing habitat for crayfish.
Table 5 Swamp gully transect comparisons.
Transect
Substrate
Burrow Density (no./m) Species diversity Surface water Conductivity* (S/cm) pH*
* Groundwater values.
Poison Gully Blackwood Rd PG1 Sandy in broad swampy area, becoming more peaty closer to, and in, stream 0.1 Gilgie, Marron, restricted Gilgie Clear Present all times 47-180 3.5 - 4.8
Milyeannup Bk Milyeannup Rd MB4 White-grey Sandy clay
Rosa Brook Mowen Rd RB3b Light brown Loam/clay
0.5 Gilgie, Koonac, restricted Gilgie Clear Dry March 307-381 4.4 - 6.1
2.6 Gilgie Clear Present all times 425-860 5.4 - 5.7
Tributaries: Tributaries of larger streams were also monitored. There were three flowingwest(Table6)andtwoflowingeast.Theeasternflowingtributariesarealso 163
twooftheswampgullies,MilyeannupBrook(MB4)andRosaBrook(RB3b)andare discussedabove(Table5).Thewestflowingtributariesallreceivedrunoffonly,had similarwatercharacteristicswithlowconductivityandalldriedupduringsummer. Only Gilgies were found in these habitats. Burrow density was low in Layman Brook,likelyduetothedominanceoftherockysubstrate.
Table 6 West flowing tributaries.
Transect
Creek substrate Burrow Density (no./m) Species diversity Surface water Conductivity (S/cm)
Layman Brook Denny Rd LB1b Rocky with gravel patches 0.4 Gilgie Clear Dry Nov 262-549
Rosa Brook Crouch Rd RB2b Silt, clay and rocky patches 2.6 Gilgie Clear Dry Jan 226-280
McAtee Brook Crouch Rd MC2b Clay with rocky patches 3.0 Gilgie Clear Dry Nov 239-520
Burrowingactivityandmigratorybehaviourofspecies
Somegeneralisationscanbemadeaboutthebehaviourofeachspeciesencountered inthisstudy. Cheraxcrassimanus The restricted Gilgie4 was found in Poison Gully, Milyeannup Brook, and McAtee Brook; these were the only permanent, fresh creeks under investigation. No clear informationconcerningtheburrowingbehaviourofthisspeciescouldbe discerned from the data gathered. However, the Poison Gully site, and to a lesser extent the Milyeannup Brook site, appear to contain significant populations of this species, suggesting that the populations may be regionally important (see Section 1). They may be significant source populations for the region, given that past studies have foundlownumbersofthisspeciesintheBlackwoodRiverchannelinthevicinityof the Yarragadee discharge, in McAtee Brook (like this study), and in Red Gully (see alsoSection1).Thesepossibilitiesraisequestionsaboutthegeneticdistinctivenessof the populations, and the overall population sizes in the two perennial tributaries withintheYarragadeeDischargeZone. Cheraxpreissii TheKoonacwasonlyfoundatoneofthetransects(MB4),whereitcooccurredwith twootherburrowingspecies.Ofallthefourspeciesfoundinthisstudy,itistheone thatislesslikelytobefoundinsurfacewatersduringdrierseasons,andtheonethat ismorelikelytodominateassemblageswherewatertablesfluctuatemoremarkedly,
The common name restricted Gilgie is used her to denote the ecology of the species, not its genetic affiliations. While it has some attributes of the habitat utilisations of the Gilgie, genetically it is more closely aligned to the Koonac C. preissii.
4
164
andthisiscertainlythecaseforthehabitatatthistransect,intheextensiveswamp system at the headwaters of the Milyeannup Brook. However, it has also been found,albeitinverylownumbers,fromRosaBrookandMcAteeBrook(seeSection 1). Cheraxquinquecarinatus Perhaps the clearest data on the burrowing and migratory behaviour in this study were found for this species, and this is due to the fact that it was the only species found in some transects so the burrowing activities in those transects could be ascribedtothisspeciesexclusively. Tributary sites receiving seasonal runoff waters only (see Table 6) showed clear relationships between declining water levels and increasing burrowing activity. Observations were made of juvenile Gilgies in the leaf litter on the creek bed after burrows reopened in winter/spring when the creeks refilled, and an absence of mature individuals at that time. These observations and recordings are together consistentwiththeideathatmatureGilgiesmigrateupthetributariestobreed(see alsoSection1)andthenburrowinforsummer,andmovedownstreamintothemain channelagainuponemergence,leavingthetributaryasanurseryfor0+ageclasses. The degree to which this species relies on these ephemeral creek systems is unknown, but the movement of Gilgies out of main channel systems (like the Blackwood River) and into more ephemeral creeks to breed, needs some more sophisticatedinvestigation. Interestingly,thepresenceofMarron,restrictedGilgiesaswellasGilgiesinthemain channelatMcAteeBrook,butonlyGilgiesinthetributaryissuggestiveofaspecies specificuseageofthistributaryresource. Cheraxcainii OnlysmallimmaturespecimensofMarronwereencounteredinthisstudy,inPoison Gully,MilyeannupBrook,andMcAteeBrook;theseweretheonlypermanent,fresh creeks under investigation, confirming the fact that Marron are not known from ephemeral systems, and that they are poor burrowers. However, in all of these systems, refuges for times of very low waters, and shelter from predation, were evident,includingshallowburrowsinthebank,andpoorlydefinedburrowsunder rocks and logs. The movement of this and other crayfishes out of the Blackwood river channel and into these small tributaries (and vice versa) was examined in Section1.
165
DISCUSSIONANDRECOMMENDATIONS
The tributaries of the Blackwood River on and around the Yarragadee Discharge ZoneappeartobetypicalburrowinghabitatforsouthwesternAustralianfreshwater crayfish, displaying the broad range of physiographic habitat characteristics where crayfish shelter and burrow: permanent to ephemeral systems, creek banks, deep pools, shallow seasonally filled ponds and floodplains, clayey to sandy and rocky, organictomineralsediments,andthepresenceofcoarsewoodydebris.Ingeneral,in termsoffreshwatercrayfish,themorespeciesrichsitescontainedpermanentwater, andagreatervarietyofthesehabitatfeatures. Fourspeciesoffreshwatercrayfishhavebeenidentifiedinthisstudy(Marron,Gilgie, restricted Gilgie, and the Koonac). Thus far no individuals of the burrowing freshwater crayfish genus Engaewa have been found in the Yarragadee Discharge Zone,orclosetoit,eventhoughsomehabitatshavelookedparticularlysuitablefor them(forinstancethesiteatRB3).Highestspeciesdiversitywasfoundinstreamsin the YADZ, namely Milyeannup Brook and Poison Gully, as well as one outside of thiszone,McAteeBrook. It should be noted that the approach used in this study, namely to investigate the potentialforburrowingactivitiesoffreshwatercrayfishtobeusedasanindicatorof the effects of groundwater declines, has never been attempted before, and this researchthereforesoughttopioneermethodologies.Aswithallpioneeringstudies, not all methods chosen were successful, and some problems in data interpretation emerged. Twoconspicuousgeneraltrendsareobservedinthedata: 1. Measurements of the number of burrows increase as surface waters recede and measures of burrowing activity (proportions of burrows with pellets or plugs)increaseaswaterlevelsrecede. 2. Thefirstobservationislikelytobeinpartameasurementerror,sincereceding waters expose sediments where burrows can be more easily observed. The second observation is more significant, and is likely to be a reflection of the burrowingbehaviourofallspecies,sincetheymustseekrefugeduringdrier times. Monitoring burrowing activities depends on some knowledge of the species inhabitingtheburrow.Thisisnotsoimportantwherereasonableassumptionscanbe made about the species present. It is much more problematic, however, when the speciesmakingtheburrowsisnotknown.Mostofthetimedifferentspeciesdonot make species specific burrows. Perhaps Marron are an exception to this rule here, being found in shallow poorly formed Type 1a burrows almost exclusively. Distinguishing between burrows of the other three species is usually almost impossible.Todeterminetheidentityoftheoccupantrequireseitherdestroyingthe 166
burrow,orwaitingforittoemerge,captureitidentifyitandreturnittotheburrow. The first was not feasible on the transect because burrows are deep and too much disturbance would have occurred. Capturing crayfish is a more viable option and was attempted with some limited success, but there were too many burrows to do thissystematically.Accordingly,forsometransectswheremorethanonespecieswas known to occur, it was impossible to provide information on how different species wererespondingtowaterlevelchanges. Theunusualweatherexperiencedoverthetwelvemonthstudywillalsoneedtobe considered.Theverydryautumnandearlywinterexperiencedin2006resultedina slower than usual recovery of water levels (i.e. water levels experienced in September 2005 were much higher than those found in the same months in 2006; mostpiezometerswerestilldryinJuly2006). Despite the methodological problems, the work conducted over the past year in establishing transects and documenting burrow densities shows some promise. It providessomemethodsandbaselinedataformonitoringcrayfishburrowingactivity inthefutureandcanbeusedtodocumentchangestoburrowingactivityassociated withanygroundwaterregimeshifts(thatmightoccurasaresultofclimatechange, land use change or groundwater extraction). In particular, future uses of this techniqueformonitoringtheeffectsofgroundwaterdeclineonaquaticfaunamight startwiththefollowinghypotheses: A.Ifgroundwaterdeclineisextendingbeyondhistoricalrangesthentheburrowingactivity offreshwatercrayfishwillproducesoilfromalowerstratigraphicsoillayerthanpreviously observed. AND B. If groundwater decline is extending beyond historical ranges, then periods of burrowing activitywilloccurearlierinspring,andburrowswillopenlaterintheautumnorwinter. The following is a list of questions that need to be answered to gain a better understanding of how freshwater crayfish populations might respond to changing groundwaterandsurfacewaterregimesinthefuture. 1. What is the genetic structure of populations and species and do tributaries andinparticulartheYADZoneshavegeneticallydistinctpopulations?Infact for most small burrowing crayfish in the genus Cherax, genetic typing is probably the only reliable way to identify species, and therefore to examine the relationship between surface water movements of crayfish and their burrowingactivity.Thereisaclearneedforasystematicstudyofpopulations in the region, in particular the populations of C. crassimanus, likely to be the mostsignificantlyaffectedspeciesshouldanychangesoccurtothevolumeof dischargefromtheYarragadeeAquifer. 2. Leading on from 1, a reliable distribution map for all freshwater crayfish species, but particularly Engaewa species, in the area defined by the Darling EscarpmenttotheeastandtheDunsboroughFaulttothewest,isrequired. 167
3. Howmightchangestowaterlevelsinfluencecrayfishmovementsintoandout of burrows, and can crayfish reproductive effort be diminished by declining periodsofsurfacewaterpresence?Thefirstpartofthisquestioncanbeatleast partly answered by combining the full seasonal data of burrowing activity withthedataofcrayfishpresenceinsurfacewaters(seeSection1).Thesecond part will require a more detailed investigation of reproductive energetics of burrowing freshwater crayfish (for instance comparing populations of the samespeciesexperiencingdifferentwaterregimes).
WATERCHEMISTRY
INTRODUCTION
The purpose of this small project was to investigate the water chemistry of the tributaries of the Blackwood River in the region of the Yarragadee discharge. This informationwillhelpto: - determine if the Yarragadee discharge, and water at transect sites could be chemicallycharacterised;and - determine relative contributions of the Yarragadee discharge to the water qualityoftheBlackwood. Inordertodothis mosteffectively thewaterchemistryofgroundwater,tributaries and the river itself should be examined under different seasonal conditions that amounttodifferenthydrological/flowregimes.
METHODS
Watersamplesfrompiezometers,tributariesandriverchannelwerecollected: 1. One set of samples was collected in late November/December 2005 to represent late spring moderate flows and water levels. These samples were collectedmainlyfrompiezometersandsurfacewatersalongtransectsites;and 2. One set of samples was collected in March 2006 to represent the base flows and low water levels in early autumn. These samples were collected from a more extensive set of tributaries in the region of the Yarragadee discharge zone (Rosa Brook, Layman Brook, Poison Gully, Milyeannup Creek, Red Gully, St John Brook) and Blackwood River sites above, in, and below the Yarragadeedischargezone. Allwatersamplesweretakenfromeitherjustbelowthesurfaceorfrompiezometer water siphoned out with a tube. Water was collected in a washed then acid rinsed plasticbottle,thenimmediatelyforcedthroughaWhatmanglassfibrefilter(45nm filter pore size) in a filter attachment to a syringe. The filtered water sample was preservedwithconcentratednitricacidandstoredforICPAESanalysisofelemental suite.
168
TheelementalsuiteincludedtheanalysisofAl,Ca,Cd,Co,Cu,Fe,Hg,K,Mg,Mn, Na, P, S, Si, and Zn (cations metals and metalloids). They represent total levels of theseelementsinfilteredwaterandthereforedonototherwisediscriminatebetween differentelementalspecies(ortheforminwhichtheelementsarefound).
RESULTS
Some elements were not detected in any of the water samples and were excluded from further analysis: arsenic (detection limit 0.01 mg/L), mercury (detection limit 0.02mg/L);lead(detectionlimit0.01mg/L);andselenium(detectionlimit0.02mg/L). Someelementswereonlysporadicallypresentandapartfromnotingtheirpatternof occurrence(below)wereexcludedfromfurtheranalysis: Cadmium: None of the November/December samples contained appreciable amountsofcadmium,allbeingbelowthedetectionlimitof0.0006mg/L.AllMarch 2006 samples, however, contained consistent concentrations of cadmium (between 0.0045and0.0064mg/L)withtheexceptionoftheRB3samplesatRosaBrookwhich were below the detection limit. Of interest here is that our sample blank also containedcadmium(0.0059mg/L)(suggestingpossiblecontamination). Cobalt:allsampleswerebelowthedetectionlimitof0.002mg/Lexceptfor8samples; ofthesethehighestlevels(0.0090.011mg/L)werefoundinthe3RosaBrooksamples inMarch2006. Nickel: below detection limit (0.004 mg/L) except for relatively high levels in Rosa Brook (RB3 creek in December 2005 and RB3 piezometer in March 2006: 0.025 and 0.021mg/Lrespectively). Phosphorus: only 4 out of 35 samples contained phosphorus levels above the detectionlimitof0.02mg/L,andthesewereall0.05mg/Lorless. ElementaldataarepresentedinAppendixBandTables7and8. March 2006 data were examined for the relationships between tributaries and river samples using the elemental suite of Al, Ca, Cu, Fe, K, Mg, Mn, Na, S, Si, Zn and conductivity.Table19showsthattheBlackwoodRiverdecreasesinconductivityasit flows through the area fed by tributaries. Most of the decline in salinity occurs downstreamofwheretheMilyeannupenterstheBlackwoodRiver.Milyeannupand Poison Gully are the freshest tributaries. The Blackwood reaches its lowest salinity downstreamofLaymanBrook(whichwasnotflowingatthetimeofsampling),after which it increases slightly in salinity (despite receiving some minimal flow from Rosa Brook). Milyeannup and Poison Gully, which are perennial and receive Yarragadeedischarge,havethehighestZn:NaratiosandhavethehighestS:(Ca+Mg) ratios. The Zn:Na ratio is proposed here as a possible chemical signature for this discharge (although the data are limited and require replication; see Recommendations). The S:(Ca+Mg) ratio is often used as a measure of the relative degreeofbufferingofawaterbody.ThehighertheS:(Ca+Mg)ratiois,thepoorerthe bufferingcapacity. 169
Theordinationofwaterchemistryshowsthedifferencebetweenthewaterchemistry of the Blackwood River proper and the tributaries during baseflow conditions in March2006,withthetwosetsofdataseparatingalltributariesinaclusteronthe left and all river sites in a cluster on the right (Figure 24). As the influence of the Yarragadee discharge increases, samples are positioned more towards the top left handcorneroftheplotforboththetributariesandtheriversamples.Thetributaries of Poison Gully and Milyeannup Brook clearly separate on the basis of their water chemistry (withZnandSplayingasignificant role).Similarly, StJohn Brook,Rosa Brook(Uppersite),andMcAteeBrookseparateandcanbedistinguishedonthebasis of their relatively highlevelsofiron(Fe)and potassium(K), possibly reflecting the ironrichwatersoftheLeedervilleaquifer. November/December 2005 samples were analysed using conductivity and the elemental suite of Al, Ca, Co, Cu, Fe, K, Mg, Mn, Na, S, Si, Zn, for a selection of surfacewaterandgroundwatersamplesfromthetransectsites.Table8presentsthe conductivity and Zn:Na ratio and S:(Ca+Mg) ratio and results are less clear than those presented for the March 2006 samples, partly due to the more heterogeneous collection of samples, and partly due to the fact that waters are complicated by surface runoff from rainfall. Tributaries and groundwater samples are all relatively fresh compared to the only Blackwood River site (BW4). This river site also had low(est) values for both ratios. The relative amounts of Zn are high in most tributariesinthesesamples.ThepiezometersampleintheupperMilyeannupBksite (MB4) had by far the highest proportion of Zn; it also had poor buffering (highest S:(Ca+Mg)ratio)andrelativelyhighlevelsofiron(Fe).IncontrasttotheMarch2006 samples, the perennial creeks of Poison Gully and Milyeannup had lower Zn:Na ratiosthanothertributaries. On the basis of water chemistry the sites separated into five different groups (Fig. 15). Data for this analysis was corrected for conductivity so as to remove concentration magnitude, leaving only the relationships between elements, their proportional representation. The water sample from Rosa Brook (Upper site on Mowen road, RB3) was the most identifiable sample, with proportionately the highestlevelsofaluminium,iron,potassium,cobalt,magnesium,silicaandsodium. NextmostidentifiablewasthepiezometersampleattheotherwisedryMilyeannup siteMB4,withthehighestconcentrationproportions ofsulphurandzinc,andhigh iron.TheheadwaterpiezometersampleinLaymanBrookisdistinct,relativelyhigh proportions of Al and K, the highest proportions of Ca and Cu, and the lowest proportionsofZn.Aheterogeneousgroupofthreesamplesarecloselyrelatedthe piezometerfromPoisonGully(whichwasveryfresh),theBlackwoodRiversample (fromwithintheYaragadeeDischargeZone),andasurfacetrickleatMcAteeCreek: theycanbecharacterisedasallhavingrelativelylowAl,Fe,Mg,KandZn.Allother samples belong to one cluster. The two Layman Brook surface water samples are almost identical, as are two surface water and two piezometer samples from the lowerRosaBrooksites. 170
DISCUSSIONANDRECOMMENDATIONS
Resultsfromthesewaterchemistryanalysesarepreliminaryonlysincerelativelyfew samplesweretakenandtheywerenotreplicatedintimeoratlocality.Nevertheless somesignificantfindingsareworthyoffurtherinvestigation: 1. Base flow water chemistry shows the potential for characterising the Yarragadee discharge,andtherebyhighlightstheimportanceofattendingtothewaterchemistry should supplementation of wetlands or creeks be required due to groundwater decline. The Zn concentrations (relative to something like Na) may be seasonally reliable,andAlisworthconsiderationinthisregardtoo. 2. The relatively high S:(Ca+Mg) ratios found for Poison Gully and Milyeannup BrooksurfacewaterinMarch2005,andtheupperMilyeannuppiezometersamplein November 2005 add further justification for an examination of the potential for acidificationofsurfaceand/orgroundwatershouldsedimentsbecomeexposeddue todroughtand/orgroundwaterdecline. Werecommendthatthefollowingpiecesofresearchbeconducted: 1. A fully seasonal and replicated series of samples from the tributary and river channel sites (as per the March 2006 sampling) across a full suite of elements (to includesignificantanions). 2. An examination of the risk of acidification due to the possible exposure of potentialacidsulphatesoils.Thiswillbebestachievedbyundertakingcoringofnear surface sediment in key creek and wetland systems in the Yarragadee Discharge Zone(particularlyPoisonGullyandtheentireMilyeannupBrooksystem).Sediments should be examined for organic content, particle size, and chromium reducible sulphurandelementalsuiteforatleasteachstratigraphiclayer.
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Table7WaterchemistrydataforMarch2006(baseflowconditions)showingsitesarrangedupstream to downstream (and where tributaries enter the Blackwood River), starting at the most upstream site on the Blackwood River near Nannup, and finishing at the Blackwood River (SuesBridge).
Site (from Upstream to Downstream) Blackwood 1 St John Bk Blackwood 2 McAtee Bk Red Gully Blackwood 3 Milyeannup Bk Blackwood 4 Blackwood 5 Poison Gully Blackwood 6 Blackwood 7 Rosa Bk U Rosa Bk L Blackwood 8
Conductivity (S/cm) 3470 735 3620 1230 960 3630 490 3420 3240 287 2570 2050 1003 674 2210
S:(Ca+Mg) 0.15 0.21 0.11 0.35 0.16 0.11 0.3 0.12 0.12 0.41 0.12 0.13 0.02 0.09 0.13
Zn:Na (x10000) 0.52 5.9 0.41 2.53 4.00 0.71 18.57 0.78 0.88 39.02 1.11 2.96 3.92 2.81 0.82
Stress: 0.0565
Blackwood River sites Tributaries

Poison Gully Blackwood River Sues Bridge
Milyeannup Rosa Bk Lower Red Gully
Blackwood River (Nannup)
McAtee Bk Rosa Bk Upper St Johns Bk
Figure24
Ordination (Semi Strong Hybrid Multidimensional Scaling using PATN) usingwaterchemistryofsamplesfromtributariesandriversamplestaken in March 2006, showing relationships between sites. Elemental suite includesAl,Ca,Cu,Fe,K,Mg,Mn,Na,S,Si,Zn.
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Table8
Water chemistry data for November/December 2005 sampling of transect sites (site codesasforreport)surfacewater(S)andpiezometergroundwater(P).
Transect/Site Conductivity (S/cm) S:(Ca+Mg) Zn:Na (x10000) BW4 3110 0.15 4.69 LB1a 364 0.31 12.65 LB1b 366 0.31 16.33 LB2 - P 230 0.14 3.00 LB2 - S 237 0.28 7.94 MB2 346 0.31 5.40 MB4 - P 307 0.75 49.02 MC2a - S CK 567 0.27 8.35 MC2a - S T 568 0.27 11.84 PG1 - P 180 0.23 3.33 PG1 - S 276 0.48 9.00 RB2a - P 247 0.43 28.29 RB2a - S 421 0.34 12.88 RB2b - P 252 0.34 14.29 RB2b - S 245 0.35 17.65 RB3 415 0.07 25.26
Row Fusion Dendrogram
0.0167 0.2322 0.4477 0.6633 0.8788
BW4 MC2a - S T PG1 - P LB1a LB1b RB2b - S LB2 - S MB2 RB2a - S PG1 - S RB2a - P RB2b - P MC2a - S CK LB2 - P MB4 RB3
Figure25
Dendrogram (agglomerative hierarchical clustering from PATN) of water chemistry showing the relationships between transect sites in November/December sampling, usingtheelementalsuiteofAl,Ca,Co,Cu,Fe,K,Mg,Mn,Na,S,Si,Zncorrectedfor conductivity (so as to remove magnitude, leaving only the relationships between elements, their proportional representation). (S= surface water, P= piezometer, or if notstatedthensurfacewater).
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APPENDICES
APPENDIXA.Transectdetails.
Transectsstartatastakeplacedontheleftbankfacingdownstreamandfinishatthepiezometerontheoppositebank. Waterway Blackwood River* Site identification Site location Stake Piezometer Length (m) o o BW4 Denny Rd S34 04.348* S34 04.382 18 St Patricks Elbow E115o30.324 E115o30.331 Gully LB1a Denny Rd S34o03.763 S34o03.751 50 Layman Brook o o E115 30.507 E115 30.528 Western flowing tributary LB1b S34o03.761 S34o03.733 o o E115 30.585 E115 30.593 Headwater LB2 Crouch Rd S34o00.905 S34o00.924 50 o o E115 30.802 E115 30.796 S34o01.430 60 Gully control MC2a S34o01.403 McAtee Brook o o E115 34.868 E115 34.849 Western flowing tributary control MC2b S34o01.396 S34o01.379 40 E115o35.128 E115o35.148 25 MB2 Brockman Hway S34o05.993 S34o06.001 Milyeannup Brook Gully Helyar Rd E115o34.187 E115o34.206 Eastern flowing tributary MB4 Milyeannup Rd S34o10.272 S34o10.305 70 E115o34.270 E115o34.259 Gully (swamp) PG1 Blackwood Rd S34o07.251 S34o07.248 40 Poison Gully E115o33.276 E115o33.302 13.2 Gully control RB2a Crouch Rd S34o01.290 S34o01.285 Rosa Brook E115o26.390 E115o26.385 Western flowing tributary control RB2b S34o01.312 S34o01.329 50 E115o27.864 E115o27.887 50 Headwater control RB3 Mowen Rd S33o55.009 S33o55.008 o o E115 28.379 E115 28.334 * This location is at the bank of the river, there is no stake at this site. It is estimated that the distance from this point to the centre of the river is 12m. 174 Type of site River
APPENDIXB.Waterchemistrydata.
Site Date Depth (m) 1.37 1.53 1.53 0.24 0.88 0.90 0.43 0.42 0.61 0.61 0.61 0.61 0.52 0.65 0.65 0.65 0.65 0.65 0.65 0.65 0.57 0.65 0.25 0.26 0.38 0.28 0.64 0.64 0.33 0.28 0.41 1.54 1.53 1.53 1.53 1.53 1.53 1.53 pH 4.61 dry dry 5.25 4.3 4.42 5.82 5.55 dry dry dry moist 5.79 dry dry dry dry dry dry dry 5.57 dry 6.00 5.81 5.95 dry dry dry 5.61 5.35 5.96 5.72 dry dry dry dry dry dry Groundwater Conductivity (S/cm) 8160 3700 7730 7700 201 186 138 475 190 169 230 125 212 1? 180 Temperature (oC) 16.3 17.0 15.0 16.0 15.4 15.3 15.5 14.9 13.3 14.6 19.2 12.5 14.2 15.8 18.2 Level (m) 10.85 10.94 10.40 10.08 10.73 1.90 2.23 2.57 2.75 dry dry 2.12 2.45 0.37 0.38 0.39 0.38 dry dry 0.35 0.35 1.12 1.07 1.22 dry dry dry 1.08 1.09 3.83 3.75 0.99 1.08 1.10 1.15 0.60 0.82 pH 6.68 6.47 6.82 7.17 7.44 6.93 6.72 5.81 6.92 5.93 6.42 6.18 6.35 5.46 6.59 6.06 6.37 6.08 6.86 6.00 6.18 5.90 5.90 5.76 5.63 5.60 5.54 5.72 5.65 6.24 Stream water Conductivity (S/cm) 3110 2600 2050 3230 7770 5980 237 241 364 508 337 373 267 262 366 436 549 420 192 194 237 207 256 272 346 456 490 472 321 317 Temperature (oC) 20.3 20.9 21.9 13.1 12.3 16.9 14.5 17.1 24.5 19.2 11.0 17.1 15.5 19.1 27.0 19.0 13.3 16.9 13.5 15.2 22.0 12.7 14.2 14.7 16.9 18.7 16.1 11.2 11.8 13.7
BW4
LB1a
LB1b
LB2
MB2
Nov 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06 Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06 Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06 Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06 Sep 05 Oct 05 Nov 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
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Site
Date Depth (m) 0.00 0.00 0.36 1.03 1.22 1.22 0.24 0.09 0.26 0.35 0.52 0.52 0.52 0.52 0.55 0.41 0.45 0.54 0.99 0.99 0.99 0.99 0.99 0.56 0.39 0.37 0.63 0.77 1.01 1.01 0.33 0.48 0.46 0.50 0.85 1.49 1.49 1.49 0.82 0.83 pH 6.05 4.58 4.38 4.65 dry dry 4.55 4.41 5.69 5.36 7.18 dry dry dry 4.47 5.54 5.03 4.30 dry dry dry dry dry 4.33 4.66 3.49 4.10 4.76 dry dry 3.90 3.96 6.10 5.50 5.40 dry dry dry 5.33 5.42
Groundwater Conductivity (S/cm) 373 330 307 381 404 391 4? 215 568 841 263 555 677 1812 132 147 180 47.1 134 173 308 260 247 422 426 Temperature (oC) 13.7 13.6 16.6 19.2 13.8 14.9 17.4 18.5 23.1 13.4 15.4 15.1 14.5 14.9 13.1 14.6 18.5 19.4 13.3 15.3 13.5 13.6 15.8 12.5 13.3 Level (m) 6.18 dry dry dry dry dry dry 1.73 1.74 1.96 1.98 2.10 1.95 1.50 1.84 1.45 1.65 dry dry dry dry 2.34 1.52 3.50 3.41 0.08 0.04 1.50 0.88 1.69 2.65 0 2.42 2.90 dry dry dry 2.80 2.89 pH 6.28 5.54 5.60 5.41 6.81 5.33 5.10 6.04 6.01 5.75 6.18 5.47 5.40 6.08 4.59 4.86 5.21 4.94 5.47 4.68 4.80 5.71 6.19 5.56 5.62
Stream water Conductivity (S/cm) 238 223 210 218 567 864 1230 990 255 487 239 255 520 294 271 276 287 287 279 280 278 356 421 453 439 Temperature (oC) 15 17.1 15.3 14.9 22.3 21.7 23.4 14.1 12.3 16.9 15.2 15.5 13.3 16.0 18.4 20.5 19.4 14.7 12.2 14.7 16.0 16.0 18.0 10.8 14.9
MB4
MC2a
MC2b
PG1
RB2a
Sep 05 Oct 05 Nov 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06 Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06 Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06 Sep 05 Oct 05 Nov 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06 Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
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Site
Date Depth (m) 0.42 0.53 0.62 1.33 1.33 1.33 0.63 0.54 0.39 0.05 0.11 0.27 0.88 0.14 0.30 pH 6.47 5.62 5.65 dry dry dry 5.35 5.37 5.52 5.46 5.71 5.44 5.7 6.42 dry
Groundwater Conductivity (S/cm) 270 224 252 272 273 425 464 583 652 860 878 Temperature (oC) 14.0 14.4 19.0 13.4 14.1 5.4 11.3 15.3 16.1 16.5 9.4 Level (m) 2.90 3.10 3.60 dry dry dry 3.00 3.10 1.80 1.70 2.10 2.16 2.26 1.90 1.62 1.73 pH 6.63 6.02 5.65 5.63 5.81 5.91 5.93 5.95 5.76 5.96 5.60 5.88
Stream water Conductivity (S/cm) 226 239 245 280 278 347 415 465 674 560 404 426 Temperature (oC) 14.1 18.4 20.4 11.2 14.8 14.6 20.0 16.0 16.5 9.6 12.8 14.8
RB2b
RB3
Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06 Sep 05 Oct 05 Dec 05 Jan 06 Mar 06 Jul 06 Aug 06 Sep 06
177
Elemental suites (mg/L) for Yarragadee study for samples collected in November/December 2005 and March 2006.
SAMPLE CODE Reporting Limit Date CBW4 - P CBW4 - S LB1a LB1b LB2 - P LB2 - S MB2 MB3 MB4 - P MC2a - S CK MC2a - S Trickle PG1 - P PG1 - S RB2a - P RB2a - S RB2b - P RB2b - S RB3 Rosa Bk (Denny) BRB Rosa Bk Milyeannup Bk McAtee Ck Poison Gully BRA Poison G BRA Milyeannup BR Longbottom St John Bk RB3 - P Rosa Bk (RB3) BRB Poison G BR Jalbarragup BR at Laymans BRA St John Red Gully Blank 26/11/2005 26/11/2005 20/12/2005 20/12/2005 21/12/2005 21/12/2005 26/11/2005 20/12/2005 26/11/2005 21/12/2005 21/12/2005 26/11/2005 26/11/2005 21/12/2005 21/12/2005 21/12/2005 21/12/2005 20/12/2005 19/03/2006 19/03/2006 18/03/2006 18/03/2006 18/03/2006 18/03/2006 18/03/2006 18/03/2006 19/03/2006 19/03/2006 19/03/2006 18/03/2006 18/03/2006 18/03/2006 19/03/2006 18/03/2006 19/03/2006 <0.01 <0.01 0.12 0.11 0.41 0.27 0.07 0.07 0.07 0.05 0.07 <0.01 0.08 0.35 0.18 0.60 0.14 2.9 0.09 0.03 0.07 0.05 0.11 0.04 0.03 0.04 0.03 3.7 0.06 0.03 0.07 0.06 0.02 0.07 0.06 0.26 0.084 2.4 2.4 2.9 1.5 2.1 1.4 1.7 2.8 1.9 0.12 1.2 1.5 1.8 1.9 1.4 2.1 12 23 2.3 2.9 1.5 36 38 41 5.3 2.3 2.8 30 41 22 39 6.9 0.31 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 <0.0006 0.0053 0.0055 0.0054 0.0055 0.0052 0.0057 0.0059 0.0059 0.0060 <0.0006 0.0052 0.0055 0.0045 0.0064 0.0046 0.0052 0.0059 0.004 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 0.011 0.009 <0.002 0.004 0.006 <0.002 <0.002 <0.002 <0.002 0.006 0.010 0.003 <0.002 <0.002 <0.002 <0.002 <0.002 <0.002 <0.001 <0.001 0.002 0.002 0.002 <0.001 <0.001 0.001 0.002 0.002 0.001 <0.001 0.001 <0.001 0.001 <0.001 0.001 0.003 0.014 0.004 0.010 0.004 0.004 0.004 0.005 0.005 0.022 0.002 0.003 0.006 0.014 0.030 0.003 0.004 0.005 <0.002 0.11 0.34 0.31 0.073 0.21 0.29 1.1 2.3 0.82 0.066 0.004 0.050 0.24 0.55 0.17 0.14 19 3.3 0.40 0.43 19 0.10 0.25 0.31 0.19 0.47 22 13 0.30 0.31 0.37 0.24 0.93 0.066 <0.05 <0.05 2.3 2.2 2.5 1.1 1.6 3.3 1.6 4.4 1.6 <0.05 0.80 1.1 2.2 1.9 2.0 6.4 9.4 5.1 4.0 8.4 0.85 6.0 6.2 6.2 9.0 9.8 5.8 5.4 6.4 4.8 5.7 7.8 0.13 0.13 0.13 6.5 6.5 5.0 3.9 6.7 7.1 5.8 11 5.1 0.056 5.0 4.1 7.3 4.2 4.1 13 24 61 8.7 20 5.1 92 99 110 16 16 12 77 110 56 61 18 0.073 <0.0002 0.0005 0.017 0.022 0.0082 0.0040 0.012 0.030 0.0054 0.090 0.0079 <0.0002 0.0011 0.012 0.036 0.015 0.0087 0.023 0.83 0.090 0.046 0.45 0.0034 0.11 0.18 0.11 0.66 0.028 0.077 0.11 0.24 0.12 0.25 0.085 0.0008 0.23 <0.05 49 49 30 34 50 57 51 79 38 27 40 35 59 35 34 95 120 280 70 170 41 420 450 480 100 120 89 350 490 260 460 130 0.99 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 0.025 <0.004 <0.004 <0.004 0.007 <0.004 <0.004 <0.004 <0.004 0.005 0.021 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.004 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02 0.03 <0.02 <0.02 <0.02 <0.05 0.12 2.8 2.8 1.1 1.5 2.7 3.1 5.6 3.7 1.9 <0.05 2.9 2.4 3.1 2.1 1.9 1.1 0.88 11 3.3 8.0 2.7 15 16 16 4.5 0.82 1.3 13 16 10 15 3.9 0.08 <0.02 <0.02 2.9 3.0 1.6 1.6 3.3 5.3 3.2 4.6 2.6 1.3 3.2 3.7 4.0 2.5 2.2 10 6.2 2.6 6.5 10 3.7 4.4 4.7 4.6 7.6 12 5.4 4.2 5.1 3.8 5.0 3.2 0.30 <0.002 <0.002 0.062 0.080 0.009 0.027 0.027 0.004 0.25 0.066 0.045 0.009 0.036 0.099 0.076 0.050 0.060 0.24 0.047 0.023 0.13 0.043 0.16 0.037 0.035 0.034 0.059 0.058 0.025 0.039 0.020 0.077 0.024 0.052 0.023 Al <0.01 Ca <0.001 Cd <0.0006 Co <0.002 Cu <0.001 Fe <0.002 K <0.05 Mg <0.005 Mn <0.0002 Na <0.05 Ni <0.004 P <0.02 S <0.05 Si <0.02 Zn <0.002
178
APPENDIX C. Crayfish collection. 5

Layman Brook LB1a Date Species Gender Size* (mm) Sep 05 C. quinquecarinatus Male 19.62 Aug 06 Male Male 22 Female 28 Female 23 Male 33 Male 30 LB1b Date Dec 05 Mar 06 Aug 06 Reproductive state Notes Inactive Immature Active Inactive Active Active Mode of capture Collected Hand Y Spotlighting Y Placed at entry to transect Trap Y At piezometer Y A few temnocephalids
Species Gender Size* (mm) Reproductive state C. quinquecarinatus 17.70 C. quinquecarinatus Female 18 Active C. quinquecarinatus Male Male <18
Notes Mode of capture Collected 3 animals sighted, 1 identified spotlight Downstream from transect Digging Y Hand Lost Hand Several more small aninmals
LB2 Date Species Gender Size* (mm) Aug 06 C. quinquecarinatus Male 32 Male 32 Male 32 Female 21 Male 27 Female 31 Male 17 Many tadpoles
Reproductive state Active Active Inactive Active Active Inactive
Notes Mode of capture Collected Soft shell, R claw regenerating spotlight Y Soft shell, L claw regenerating Dark colour Y Trap R claw regenerating Hand
Size is measured as ocular carapace length (OCL).
179
Milyeannup Brook MB2 Date Species Dec 05 C. cainii Mar 06 C. quinquecarinatus C. crassimanus Several fish species, incl. G. occidentalis and a small perch C. quinquecarinatus
Gender Female Female Male Female
Size* (mm) Reproductive state Notes 26.5 Immature 7.90 In leaf litter 15.38 17.26
Mode of capture Collected spotlight Spotlight dig
Jul 06
C. cainii C. quinquecarinatus C. crassimanus
? C. quinquecarinatus
Female Male Male Female ? Many Female Female Female Female Female Female Female Female/male Female Male Female Female
1.30 1.40 1.60 1.50 1.10 others 26 22 25 26 24 21 22 24 22 24 28 25
spotlight
small Immature Immature Trap 1 L claw missing Temnocephalids 1 temnocephalid Active Dominant claws Soft L claw regenerating Active Trap 2 Trap 3 Y
Y Y Y
180
MB2 contd Date Species Jul 06 C. crassimanus?
Gender Size* (mm) Reproductive state Notes Mode of capture Collected Female 21 Female 22 Temnocephalids Male 21
MB4 Date Species Gender Size* (mm) Dec 05 C. preissii C. quinquecarinatus Sep 06 C. quinquecarinatus Female 26.0 Male 28.0 Male 27.5 Female 32.0 Female 34.0 Female 20 Female 21.4 Many 8-12
Reproductive state Active Active Active Active Active Active
Notes Half specimen Several sighted Trapped in ditches next to road
Mode of capture Collected Hand Y Spotlight Trap 1 Y Trap 2
Plugged type 2 burrow, water 36cm below surface ditches next to road
Digging Hand
Y Y
181
McAtee Brook MC2a Date Species Gender Size* (mm) Dec 05 C. quinquecarinatus Several Jan 06 C. quinquecarinatus 4 1 C. cainii Other species 1 Jul 06 C. crassimanus Female 23 Male 22 Male 22 Female 26 ? Female 20 C. crassimanus Male 22 32 C. quinquecarinatus Female No animals
Reproductive state Notes In dam In dam In dam Active Active Active Active Active Active
Mode of capture Collected Spotlight Spotlight Spotlight Trap in dam Hand Trap in dam Trap in pool
L claw tip of propus missing L claw regenerating L claw regenerating Hairy
Y Y Kept
MC2b Date Species Gender Size* (mm) Aug 06 C. quinquecarinatus Female 27 Female 24 Male 30 Female 11 ? 10
Reproductive state Notes Mode of capture Collected Active Trap Y Inactive Active Y R claw regenerating Hand Y L claw missing Y Many small animals in leaf litter
182
Poison Gully PG1 Date Species Gender Size* (mm) Reproductive state Dec 05 Jan 06 C. quinquecarinatus Several unidentified Mar 06 C. crassimanus Male 21.12 one ? Galaxias occidentalis Jul 06 Male 30 Male 21 C. quinquecarinatus Male 24 Male 26 Female 25 Female 24 C. cainii Male 30 C. quinquecarinatus Male Nightfish Male 22 ? Male 22 Male 21.5 Male 20.0 C. quinquecarinatus ? Female Male Male Female Female 21 22 28 21 20.5
Notes No crayfish found
Mode of capture Collected Spotlight Hand Spotlight
R claw regenerating
Trap 1
Y Y
R claw regenerating Spines on telson R claw missing Trap 2
Y Y
Y Y L claw missing Main channel upstream Trap 3
R claw & L5th leg regenerating
183
Rosa Brook RB2a Date Species Gender Size* (mm) Dec 05 C. quinquecarinatus Mar 06 C. quinquecarinatus Female 11.30 Male 10.52 Male 11.58 Male 11.90 Female 24.46 Aug 06 C. quinquecarinatus Male 24.00 Female 30.00 Male 18.00 Many sighted
Reproductive state Notes Mode of capture Collected Sighted only spotlight Single burrow Digging Y
Inactive Inactive Inactive
Cut in half Under log Wet night
spotlight
RB2b Date Species Gender Size* (mm) Aug 06 C. quinquecarinatus Female 16.00 Male Female 20
Reproductive state Notes Mode of capture Collected Inactive Hand Y Active Large animal Spotlighting Inactive L claw missing Y
184
RB3a Date Species DecC. quinquecarinatus Jan 05 Jul 06 C. quinquecarinatus
Gender
Size* (mm) Reproductive state Notes In dam
Mode of capture Collected trap Traps Traps Y
Female Female Female Female/male Female/male
28.00 22.00 34.00 26.00
In dam, soft shell Some temnocephalids R claw missing
RB3b Date Species Gender Size* (mm) Repro-ductive state Notes Mode of capture Collected Mar 06 None found 3 burrows digging Jul 06 C. quinquecarinatus Female/male Traps Y Nightfish
185

Fish and Crayfish Completed)

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Fishandcrayfishcommunitiesof theBlackwoodRiver:migrations, ecology,andinfluenceofsurface andgroundwater

Fishandcrayfishcommunitiesofthe BlackwoodRiver:migrations,ecology,and influenceofsurfaceandgroundwater

Section 2 Crayfish burrowing activity in the region of YarragadeeDischargeZone,BlackwoodRiver... 140

Jalbarragup Milyeannup Pool

1.0 0.9 0.8 0.7

Lower Blackwood River 609-1362

Study period Long term (1887-2004)

Monthly rainfall during study Long term monthly rainfall (1887-2004)

Water temperature (C)

5 Nov Jan Mar May Jul Sep

Denny Rd Milyeannup Pool Jalbarragup Quigup

Denny Rd Milyeannup Pool Jalbaragup Quigup

7.5 7.0 6.5 6.0

5.5 5.0 4.5 4.0 3.5 Oct

Figure10 MeanpH(1S.E.)atthesamplingsitesinthetributaries.N.B.theincreased acidityinRosaBrookduringthedryperiodinMarchandJune2006.

Figure11 MeanpH(1S.E.)atthesamplingsitesinthemainchanneloftheBlackwood River.

Dissolved oxygen (ppm)

Dissolved oxygen (ppm)

Mean discharge (m 3/sec)

Nannup Darradup Gingilup Hut pool

Mean number of fish

1200 1000 800 600 400 200 0

Mean number of fish

1200 1000 800 600 400 200 0

Mean number of fish

1200 1000 800 600 400 200 0

Upstream and downstream movement of Freshwater Cobbler at the four mainchannelsites.NS=notsampled.

Downstream movement Upstream movement

Mean number of fish

Mean number of fish

Mean Gonadosomatic Indices (+1SE)

log10 mean frequency of fish

0.5 1.0 1.1 1.2 1.3

log10 mean temperature ( C)

log10 mean frequency of fish

0.0 1.0 1.1 1.2 1.3

log10 mean temperature ( C)

log10 mean frequency of fish

1.8 -0.05 0.00 0.05 0.10 0.15

log10 mean discharge (M /sec)

Table2 CorrelationsbetweenoverallmeanupstreamanddownstreammovementsofFreshwaterCobberinthe mainchannelsitesoftheBlackwoodRiverandprevailingenvironmentalvariablesduringthemigration period(NovembertoJuly).N.B.Datawerelog10transformed,*denotescorrelationissignificantatthe 0.05level(2tailed).

Denny Road Milyeannup Pool Jalbarragup Quigup TOTAL (%)

Downstream movement Upstream movement

Mean number of fish

Mean number of fish

600 500 400 300 200 100 0

Mean number of fish

Mean number of fish

Total length (mm)

Total length (mm)

0 10 20 30 40 50 60 70 80 9 100 110 120 130 140 150 160 170 180 0

Total length (mm)

0 10 20 30 40 50 60 70 80 9 100 110 120 130 140 150 160 170 180 0

Total length (mm)

Western Minnow (G. occidentalis)

Mean number of fish

Mean number of fish

ry er er er ch tob emb emb brua Mar v c Oc Fe No De

Western Minnow (Galaxias occidentalis) Milyeannup Brook

2006 February NOT FLOWING

Total Length (mm)

Total Length (mm)

Western Minnow (Galaxias occidentalis)