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639.313 MONTANASTATELIBRARY F2brd 2003 30864 1002 1203 7 FISHERIESDIVISION FederalAidJobProgressReport MontanaStatewideFisheriesManagement FederalAidProjectNo:F-l13-R1,R2,R3 FiscalYear:July1,2000-June30,2001 July1,2001-June30,2002 July1,2002-June30,2003 STATEDOCUMENTSCOLLECTION ProjectTitle:StatewideFisheriesManagement JobTitle: BitterrootRiverDrainage JUN 20 2003 PPrroojjeeccttNReupmobretri:ng3P2e2r0iod:January1,2001-December30,2002 MHFoLn/tNaAnaM|OtN^TAeNA5R9A6R2Y0 ABSTRACT BitterrootRivertroutpopulationsoverallareholdingupwelldespitetwoyearsofsevere droughtin2000and2001,andthepresenceofwhirlingdiseaseinfectionsintheupper river. Westslopecutthroatpopulationshaveincreasedsincerestrictivefishingregulations wereimposedin1990andrainbowandbrowntroutpopulationsarewithinthenormal rangeofpastmonitoring.Theparasiteassociatedwithwhirlingdisease,Myxobolus cerebraliswasfoundinhigherdensitiesintheupperriverparticularlytheEastFork Bitterroot..Throughradiotelemetry,wewereabletoidentifyspawningareasusedby fluvialwestslopecutthroat.Westslopecutthroatusedavarietyofstreams,buttheNez PerceForkiswheremostfromtheWestForkBitterrootandupperBitterrootRiver spawned.BigCreekhasalsobeenidentifiedasanimportantspawningtributaryfor cutthroatxrainbowtrouthybrids. FishpopulationmonitoringontheBitterrootNationalForestindicatesthatpopulation trendsvarythroughoutthedrainage.Nooveralltrendisapparent,exceptthatthefiresof 2000andresultingwatershedinstabilityhavecauseddebrisflowsandincreasedwater temperaturesinsomereaches.Thedebrisflowshavehadseriousimpactstothefisheryin somestreams.Fishingregulationrestrictionsappeartobehavingapositiveeffectin SkalkahoandDalyCreeks..ThelongtermmonitoringofwatertemperatureinBitterroot drainagestreamscontinuestoprovideadatabasethatisusefulforcomparisonsbetween streams.Afewmoresiteswereaddedtothegeneticsdatabase,whichisprimarilyusedto identifythelocationsofpureandhybridizedpopulationsofwestslopecutthroat. ThestockingofLakeComowithkokaneehashadmixedsuccess.Earlysurvival appearedtobehigh,howeverrecentsamplinghasnotidentifiedmuchadultsurvivalor spawning.Stockingofkokaneewillbediscontinued. 1 r TABLEOFCONTENTS BACKGROUND 4 METHODS 5 RESULTSANDDISCUSSION 6 BitterrootRiver 6 RainbowTrout 8 BrownTrout 1 WestslopeCutthroat 14 LowerWestForkBitterroot 16 LowerEastForkBitterroot 18 WhirlingDisease 20 RadioTelemetry 21 SkalkahoCreekDitches 23 BitterrootNationalForest 26 WaterTemperature 34 GeneticTesting 35 LakeComo 38 LITERATURECITED „.39 3 BACKGROUND TheBitterrootRiverflowsinanortherlydirectionfromtheconfluenceoftheEastand WestForksnearConner,Montana.Theriverflows84milesthroughirrigatedcropand pasturelandtoit’sconfluencewiththeClarkForkRivernearMissoula,Montana.Five majordiversionsandnumeroussmallercanalsremovesubstantialquantitiesofwater fromtheriverduringtheirrigationseason(Spoon1987).Inaddition,manyofthe tributaries,whichoriginateontheBNFaredivertedforirrigationduringthesummer monthsandcontributelittlestreamflowtotheriverduringthattime.Therefore,many tributariesandthemainstemoftheBitterrootRiverarechronicallydewateredduringthe irrigationseason.StreamflowcharacteristicsvaryalongtheBitterrootRiver,withthe mostcriticallydewateredreachbetweenHamiltonandStevensville(Spoon1987).To helpalleviatethemainstemdewatering,theMFWPannuallysupervisesthereleaseof 15.000acre-feetofwaterfromPaintedRocksReservoirontheWestForkofthe BitterrootRiverand3,000acre-feetofwaterfromFakeComo.Urbanizationand associateddevelopmentofthefloodplainisincreasingintheBitterrootValley(Javorsky 1994). TheBitterrootRiverisanimportantsportfisheryforanglersinwesternMontana. PressureestimatesfromthestatewidesurveyindicatethattheBitterrootRiversupported andestimated110,931and104,144anglerdaysduring1999and2001,despitesignificant turbidityin2001(McFarlandR.C.andD.Meredith2000,2002).Thesefiguresindicate anincreasingtrendinanglingpressureontheBitterrootRiver. Duetothisincreasing pressure,fishingregulationshavebecomemorerestrictiveinrecentyearstoprotectthe adultfish.Acreelcensuswasconductedin1992and1993toassesstheseimpacts. Overall,itindicatedthatfishingharvestwasnothavingaseriousimpactonthe populationoftroutbutthatmonitoringshouldcontinue(Clancy1993).Anglingpressure hasnearlydoubledsincethatcreelcensus.ABitterrootRivermanagementplanis overduesincetheoriginal5yearplanwaswrittenin1991(MFWP1991). DuetotheimportanceofunderstandingconnectionsbetweenBitterrootRiversalmonids andtheirspawningareasweimplantedradiotransmittersinwestslopecutthroattrout OncorhynchusclarkilewisifromtheBitterrootRiverin2001and2002.Wefollowed thesefishtoidentifyspawninglocations. StreamswithintheBitterrootNationalForest supportwidespreadpopulationsofnativewestslopecutthroatandbulltrout.Duetothe importanceofstreamswithintheBitterrootNationalForest(BNF),wehavealso monitoredfishpopulationsthere.TheBitterrootNationalForestencompasses1.6million acres,71%ofwhichisinMontana.Threemountainranges,theBitterrootstothewest, theSapphirestotheeast,andtheAnaconda-Pintlarstothesoutheastcomprisethe BitterrootNationalForest.WaterflowingwithintheBNFisexcellentinqualityandmost isconsideredsoft,aresultofbasingeology.StreamsoriginatingfromtheBitterroot Mountainsareunusuallylowinhardnessanddissolvedsolidsbecauseottheresistant igneousandmetamorphicrocks.ThestreamsdrainingtheSapphirerangetendtohave higherdissolvedsolidsbecauseofslightlylessresistantandmoresolublebackground 4 , * geology(GamandMalmgren1973).WithinMontana,theBNFistheheadwatersofthe BitterrootRiver. During2000,wildfiresburnedsignificantacreagesintheBitterrootdrainage.Itis estimatedthat356,000acreswereburned.Studiesoftheimpactsofwildfireonfisheries indicatethatinhealthysystems,mostnegativeimpactsareshort-term(Gresswell1999). Sincewildfireimpactshavebeenwidelystudied,wedidnotfocusourworkonassessing theseimpacts.However,agraduatestudythroughMontanaStateUniversityis researchingtheimpactsofthefiresonnativeandnon-nativetrout. Historically,LakeComohasbeenstockedwithvariousspeciesoffish.Inthepastdecade catchableandbroodrainbowtrouthavebeenstockedannually.Duetothetluetuating waterlevelsinthereservoir,growthandsurvivalhasbeenpoor.Beginningin1997, kokanee,Oncorhynchusnerka,werestockedasfingerlings,inanattempttoaddsome varietyfortheanglersandstudywhetherkokaneewouldgrowfasterthanrainbowtrout. METHODS FishpopulationestimatesontheBitterrootRiverwerecollectedonseveralreachesover thepast19years.Studyreacheswereselectedbasedonhistoricaldata,streamfiow patternsandfishingregulations.Thereachesare2.2-5.1milesinlength.Electrofishing wasconductedfroma14-footlongaluminumdriftboatfittedwithaboomshocking system.Thesystemwaspoweredby5000-wattgeneratorandcurrentwasmodified throughaCoffeltMarkXXIIelectrofishingunit.Smoothdirectcurrentwasusedto capturefish.ThePetersonmark-recapturemethodwasusedtocalculatepopulation estimatesasmodifiedthroughtheMontanaFish,WildlifeandParksmark-recapture program.Severalmarkandrecapturerunswererequiredtoobtainsufficientsamplesize toestimatefishpopulationsinsomereaches.Inrecentyears,mostofthefishcollections downstreamofHamiltonhaveoccurredatnighttofacilitatehandlingofmorefish.The populationestimateswerecollectedduringSeptemberandOctobereachyear.Brown troutmaybemigratingbyOctober,therefore,theirestimatesmaybeinflated. During2001and2002sentinelcageswereusedtoassessthepresenceanddegreeof whirlingdisease.PersonnelfromtheBozemanofficeofMFWPinstalledthecageswith thehelpofregionalpersonnel.During2001wemonitoredcagesthroughoutthe BitterrootRiversystemandduring2002weconcentratedontheEastForkBitterroot River. Radiotransmittersweresurgicallyimplantedintowestslopecutthroatduringthespringof 2w0e0r1ecaanpdtu2r0e0d2bienttwheeemnaAinngslteermsoRfootshteBaintdteWrorooodtsRiidveerb.eIfnor2e00t1he,y1b5ewgeasntsthleoiprescpuatwthnrionagt migration.In2002,10westslopecutthroat,betweenBellCrossingandStevensville,were capturedandtransmitterswereimplanted.Thetransmittersandreceiverswereprovided byAdvancedTelemetrySystems(ATS).Thetransmittershadanexternalantennaethat 5 protrudedanteriortotheventofthefishaftersurgery.Theweightofthetransmitterswas bWeetwfeoelnlo8weadndth1e1figsrhaumssinagndanthAeTfSreq1u6e-cnhcaynrnaenlgfeiwealdsma4s0t.e4r0r0ecaenidve4r0..A5f6t0erthe transmitterswereimplanted,weattemptedtorelocatethefishatleastweeklyuntil spawninganddownstreammigrationended. AvarietyofditchesdivertwaterfromSkalkahoCreek.Someoftheditchesdivertwater andfishdirectlyfromthecreekwhileothersmixBitterrootRiverwaterandSkalkaho Creekwaterbeforedivertingitfromthecreek.Fourditchesweresampledin2001-2002 toassessthenumberoffishpresentintheupperendoftheditchesduringlatesummer andearlyFall.TheHedgeditch,whichmixesriverandcreekwaterwassampledwitha screwtrapduringSpringthroughFallof2002toassessthedownstreammovementoffish intotheditch. WemonitoredfishpopulationsinsomestreamsontheBitterrootNationalForest. Backgroundworkthatwentintoselectionofthestudysitesisdescribedinprevious reports(Clancy1993,1996).Duetotheseverityandlargegeographicscaleofwildfires ontheBitterrootNationalForestin2000weselectedoursitestoassesssomeofthe futureimpacts.Mostofthesiteschoseninthepastfewyearsarelongtermmonitoring sitesestablishedpreviously.Fishwerecapturedbyelectrofishingusingsmoothdirect current.Onlargerstreamsabankelectrofishingunitisusedpoweredby4500watt generatorandcurrentiscontrolledthroughaCoffeltVVP-15unit.Onsmallstreamsa backpackshocker,theCoffeltMark10,wasused.Weestimatedtroutpopulationson monitoringreachesusingamark-recapturetechnique.Monitoringsectionsareusually 1000feetlong.Onthemarkingrun,fisharereleasedasclosetotheircapturesiteas possibleandapproximatelyoneweekisallowedbetweenmarkandrecapture.Population estimatesarecalculatedusingtheMontanaDepartmentofFishWildlifeandParksMark- Recaptureprogram. Westslopecutthroatwerecollectedatsomesitesforelectrophoreticanalysis.Allfish weresenttotheUniversityofMontanaforanalysis. StowawayrecorderswereplacedinstreamsinlateJuneandearlyJulyofeachyear.They wereremovedinmid-Octoberandthedatawasdownloadedforanalysis.Wecharted eachdatasetandcalculateddegreedays(definedastheaveragedailytemperaturein degreescentigradesummedfromJuly18toOctober1eachyear). RESULTSANDDISCUSSION BitterrootRiver During2001 troutpopulationestimateswerecollectedfromtwosectionsofthelower EastFork oftheBitterroot River, andtheHamilton and Stevensvillesections ofthe BitterrootRiver.During2002,onepopulationestimatewascollectedfromeachofthe lowerEastForkandWestForkoftheBitterrootRiver.Also,in2002,atroutpopulation estimatewascollectedontheDarbysectionoftheBitterrootRiver(Figure1). 6 •MISSOULA LOLO• 1 FIGURE1.MapofelectrofishingsectionsontheBitterrootRiversampledduring 2001or2002. RainbowTrout TherainbowtroutestimatesinthemainstemoftheBitterrootRiverindicatelowerthan averagepopulationsof8-12inchfishandaveragetoaboveaveragenumbersoflarger rainbowtrout(Figures2-7).Thenumberof8-12inchfishatDarbyandHamiltonismuch lowerthanaveragecomparedtopastestimates.AtStevensvillethenumberof8-12inch fishwaswithintherangeofpastestimates.Whirlingdiseasewasdetectedwithhigher infectionratesintheupperriverthanpastyearsand2000and2001weredroughtyears thatcouldhaveimpactedthesurvivalofyoungeryearclasses.Atthistime,itisnot possibletodetermineifwhirlingdiseaseisresponsibleforthedecreaseinsmallerfish.In theHamiltonandStevensvillesectionstheinfectionrateofwhirlingdiseasehasbeenlow tonon-existent.Thelargerfishover12inchesarewithinthenormalrangeofpast estimatesatallthreestudylocations. Bitterroot River-Darby RainbowTrout 2002 099 2500 96 2000 95 1500 H93 1000 90 500 89 0 85 83 82 5F.i0guarned29..9PoipnuclhaetsiodnureisntgimtahteeyseoafrsraiinndbicoawtterdoutintheDarbySectionbetween 8 Bitterroot River-Darby Rainbow Trout 2002 99 96 95 ii93 90 89 85 83 Figure3.PopulationestimatesofrainbowtroutintheDarby 82 sectionlargerthan10inchesduringtheyearsindicated. 9 Bitterroot River-Hamiiton RainbowTrout SizeClass(inches) Figure4.Populationestimatesofrainbowtroutbetween8.0and11.9incheson theHamiltonsectionoftheBitterrootRiverduringtheyearsindicated. 9 Bitterroot River-Ham ilton Rainbow Trout Figure5.Populationestimatesofrainbowtroutover12.0inchesintheHamilton sectionoftheBitterrootRiverduringtheyearsindicated. € Bitterroot River-Stevensville Rainbow Trout 2001 H 500 96 400 94 300 93 200 100 90 0 10 11 12 89 SizeClass(inches) Figure6.Populationestimatesofrainbowtroutbetween8.0and12.9 inchesintheStevensvilleSectionoftheBitterrootRiverduringthe yearsindicated. c 10 Bitterroot River-Stevensville Rainbow Trout 2001 96 94 93 l»91 90 89 Figure7.Populationestimatesofrainbowtroutover13inchesintheStevensville sectionoftheBitterrootRiverduringtheyearsindicated. BrownTrout Duetothetimeofyearwecollectpopulationestimatesspawningmigrationshavelikelybegunandthis couldbiasourpopulationestimates.Therefore,browntroutpopulationestimatesaremoreofanindexthan numericestimate.Browntroutpopulationshaveremainedstableinthe3studysections(Figures8-13). Bitterroot River-Darby Brown Trout 2002 99 1000 96 800 93 N/I000' 640000 EH90 200 89 0 85 84 83 Figure8.Populationestimatesofbrowntroutbetween6.0and10.9inchesin theDarbysectionoltheBitterrootRiverduringtheyearsindicated.