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s 639.3755 F2fsu 2001 Fish Surveys of the Upper South Fork Judith River and Tributaries its Conducted during 2000 Bradley B. Shepard Montana Fish, Wildlife and Parks and Montana Cooperative Fishery Research Unit 1400 South 19'^ Bozeman, Montana 59718 y October 2001 1 Soulli Kork.fiidilli 2000 Table ofContents Table ofContents ii List ofTables ii List ofFigures iii Executive Summary v Introduction 1 Study Area 1 Methods 1 Results 5 Big Hill Creek 5 BluffMountain Creek 15 Cabin Creek 18 Cross Creek 21 Deadhorse Creek 22 Russian Creek 24 South Fork Judith River 28 Smith Creek 31 Discussion 33 Fish Distribution and Abundance 33 Recommendations for Conservation ofWestslope Cutthroat Trout 34 Acknowledgements 34 References 34 List ofTables Table 1. Catch ofwestslope cutthroat trout (WCT) and rainbow trout (RB) per electrofishing pass, estimated number per section (standard error; S.E.), and section length (m) by stream, stream kilometer (Km) and date during 2000 in the upper South Fork Judith River 6 Table 2. Average length and weight (ranges) offish captured during fish sampling in the upper South Fork Judith River and its tributaries by stream and stream kilometer 7 Table 3. Streambed composition, frequency ofsmall (< 150 mm) and large (>= 150 mm) in- channel and cross-channel woody debris per km, and square meters ofspawning habitat per km by stream, section, and date 1 Table 4. Total length (m), average length (m), average width (m), average depth (cm), and average volume (cubic meters) ofeach habitat type and average thalweg depth (cm) and residual pool volume (cubic meters) by stream and section 12 Table 5. Rankings (0 = none or lowest; to 9 = highest) ofinstream cover, bank cover, bank stability, and pool quality by stream, section, and date 15 Page ' ii Su'jjh Kork.ludith 2000 List ofFigures Figure 1. Map ofupper South Fork Judith River drainage showing locations ofthermographs, sites offish abundance sampling (coded by fish species observed or captured), and stream kilometers (upstream from mouth) during 2000 2 Figure 2. Map ofstreams sampled in upper South Fork Judith River drainage showing stream names and sample sites, by type ofpopulation abundance information collected 3 Figure 3. Average, minimum, and maximum water temperatures in Big Hill Creek immediately below the unnamed tributary during the summer of2000 5 Figure 4. Length frequencies ofwestslope cutthroat trout captured in Big Hill Creek during 2000 6 Figure 5. Average, minimum, and maximum water temperatures in BluffMountain Creekjust above its mouth during the summer of2000 16 mm Figure 6. Relative abundance (number offish 75 and longer captured on the first m electrofishing pass per 100 ofstream length) forwestslope cutthroat (WCT), brook (EBT), and rainbow and rainbow/cutthroat trout hybrids (RB + HB) in four sections of BluffMountain Creek and three sections ofan unnamed tributaryby stream kilometer. 17 Figure 7. Length frequencies for westslope cutthroat trout in BluffMountain Creek (by stream kilometer up from mouth) and in three sections in a major unnamed tributary (TRIB) during July 2000 18 Figure 8. Average, minimum, and maximum water temperatures in Cabin Creekjust above its mouth during the summer of2000 19 mm Figure 9. Relative abundance (number offish 75 and longer captured on the first electrofishing pass per 100 m ofstream length) for westslope cutthroat (WCT) and rainbow and cutthroat/rainbow trout hybrids (RB + HB) in eight sections ofCabin Creek by stream kilometer 20 Figure 10. Length frequencies forwestslope cutthroat trout in Cabin Creek (by stream kilometer up from mouth) during late June (km 1.6 and 3.2) and late July (km 0.8, 2.4, and 4.0 to 6.4) 2000 20 Figure 11. Length frequencies forwestslope cutthroat trout in Cross Creek at stream kilometer 0.8 during late July 2000 21 Figure 12. Average, minimum, and maximum water temperatures in Deadhorse Creekjust above its mouth during the summer of2000 22 mm Figure 13. Relative abundance (number offish 75 and longer captured on the first m electrofishing pass per 100 ofstream length) for westslope cutthroat trout in six sections ofDeadhorse Creek by stream kilometer..... 23 Figure 14. Length frequencies for westslope cutthroat trout in six sections ofDeadhorse Creek (by stream kilometer) during late July 2000 24 Figure 15. Average, minimum, and maximum water temperatures in Russian Creekjust below the South Fork Road crossing (top) andjust above its mouth (bottom) during the summer of2000 26 mm Figure 16. Relative abundance (number offish 75 and longer captured on the first m electrofishingpass per 100 ofstream length) for westslope cutthroat trout during 2000 in two sections ofRussian Creek (left) and an unnamed tributary to Russian Creek (right) by stream kilometer. 27 Page iii South Fork Judith 2000 Figure 17. Length frequencies for westslope cut throat trout in two sections ofRussian Creek (by stream kilometer) and its major unnamed tributary (Trib) during late June 2000. 27 Figure 18. Average, minimum, and maximum water temperatures in the South Fork Judith River below the mouths ofBluffMountain Creek (top), Big Hill Creek (middle), and Corral Creek (bottom) during the summer of2000 29 mm Figure 19. Relative abundance (number offish 75 and longer captured on the first electrofishing pass per 100 m ofstream length) forwestslope cutthroat trout (WCT) and rainbow trout (RB + HB) during 2000 in nine sections ofthe South Fork Judith River by stream kilometer 30 Figure 20. Length frequencies for westslope cut throat trout in nine sections ofthe South Fork Judith River (by stream kilometer) during late June 2000 31 Figure 21. Average, minimum, and maximum water temperatures in Smith Creekjust above its mouth during the summer of2000 32 mm m Figure 22. Frequencies ofrelative abundance (number offish 75 and longerper 100 of stream length) for westslope cutthroat trout in allopatry in 489 sample sections that were a minimum of50 m long within the streams ofthe upper Missouri Riverbasin and a few streams in the upper Clark Fork basin ofMontana 33 Pai'c IV South ForkJudith 2000 Executive Summary This report summarizes fish survey information collected in the upper South Fork Judith River drainage in 2000. The purpose ofthe surveywas to document the status ofwestslope cutthroat trout, Oncorhynchus clarki lewisi (WCT), within the upper South Fork drainage to help direct WCT WCT conservation efforts for in this drainage. were widely distributed in the upper South Fork Judith Riverbasin and they were generally abundant where they occurred. Relative WCT mm m abundance for generally ranged from 20 to 50 fish 75 and longerper 100 ofstream WCT m WCT length and was as high as nearly 70 per 100 ofstream. in the South Fork Judith basin were found as far up into headwaters as stream size would support fish. Normative rainbow trout or fish identified as hybrids occupied the lower portions ofBluffMountain and Cabin creeks, most ofSmith Creek, and were also found in the South Fork Judith as far upstream as river km 19.3,just above Smith Creek. I am unsure how numerous rainbow trout are in the South Fork or how long they have been present in the upper portions ofthe basin, but their WCT presence so far up the basin is a major concern for conservation and restoration. The upper South Fork Judith Riverbasin above BluffMountain Creek represents a good opportunityto restore a moderately large connected stream and river system for WCT. This area contains approximately 60 km ofstream with approximately 40 km now inhabited by fish. Any attempt WCT to conserve in the upper South Fork will require construction ofa fish barrier to eliminate the continuing invasion ofbrook and rainbow trout into the upper basin. Unfortunately, rainbow trout have already made their way up into the basin at least as far as Smith Creek. It also appears WCT that populations in several tributaries, including Russian and Cabin creeks, have already been slightly hybridized with either rainbow trout or Yellowstone cutthroat trout based on earlier genetic sampling. Fin clips taken for PfNE genetic analyses during this studywill provide more WCT conclusive evidence for the genetic status ofall populations. Lastly, fish identified as WCT either rainbow or hybrids between rainbow and were captured in BluffMountain, Cabin, and Smith creeks, as well as the South Fork Judith. Thus, several decisions will have to be made regarding barrier location(s) and either management ofexisting slightly hybridized populations as conservation populations that could not be used as donors for other waters, orremoval of existing hybridized populations and replacing these existing hybrid populations using genetically pure sources from other streams in the basin, either by natural dispersal or by active human intervention. P;)uc V Soiitli 1‘orlv .Midilh 2000 Introduction The Montana Cooperative Fishery Research Unit and Montana Fish, Wildlife and Parks (FWP) was asked by Region 4 ofFWP and the Lewis and Clark National Forest to conduct fish surveys in waters ofthe upper South Fork Judith River, Montana to document the presence and status of westslope cutthroat trout {Oncorhynchus clarki lewisi; WCT). These surveys were done during 2000 in cooperation with Region 4 ofFWP and the Lewis and Clark National Forest to develop a conservation plan for westslope cutthroat trout in the upper South Fork. Study Area The streams surveyed included Corral, Big Hill, Russian, Deadhorse, Cross, Cabin, Smith and BluffMountain creeks, as well as the main South Fork Judith River down to the mouth ofBluff Mountain Creek (Figure 1). Streams in the upper South Fork supported WCT, brook trout (Salvelinusfontinalis), and rainbow trout {Oncorhynchus mykiss), while the South Fork also supported mountain whitefish {Prosopium williamsoni) and mottled sculpin (Coitus hairdi). Methods A systematic sampling scheme was employed to estimate both the relative abundance and distribution offishes and to quantify stream habitat characteristics. Sample sections ranging from 45 to 135 m were surveyed at a frequency ofapproximately every 0.8 km (0.5 mile) of stream length by single-pass electrofishing with backpack Smith-Root electrofishers (Models SR-12BP, SR-15B). At approximately 3.2 km (2 mile) intervals we conducted two-pass depletion population estimates (Van Deventer and Platts 1985; Figure 2). Population estimates were not made when few orno fish were captured during the first electrofishing pass. Sample section lengths were usually at least 20 times, with most at least 30 times, the average wetted stream width. Lyons (1992) found that when stream lengths of35 times the mean wetted width were sampled with a towed electrofishing unit, all species offish in fish communities in warm water streams ofWisconsin were generally captured. Sample sites were referenced by mile above the stream’s mouth, and later converted to kilometers above the mouth, and by latitude and longitude obtained from a global positions system (GPS; Garmin 12XL). Field GPS locations were input into an ARCVIEW (Version 3.2; 1999; Environmental Systems Research Institute, Inc.) event theme and projected on I;100,000 stream hydrography layers. The field GPS locations were corrected to overlay the hydrography layer and stream kilometer locations when discrepancies existed between field GPS and mapped locations (Figures 1 and 2). Length (total length in mm) and weight (gm) were recorded for all captured salmonids. For two- pass estimates to provide reasonable results, we assumed that field calculated probabilities of capture (calculated as 1- (C2/C1); where Ci= number captured on the first pass, and C2 = number captured on second pass) had to be 0.80 or higher (c.f White et al. 1982; Riley and Fausch , 1992). Iffield calculated probabilities ofcapture were less than 0.80 after two passes, additional electrofishing passes were usually made. Population estimates were calculated using a maximum likelihood estimator within the MICROFISH program (Van Deventer and Platts 1985) Pagf - 1 Digitized by the Internet Archive in 2017 with funding from Montana State Library https://archive.org/details/fishsurveysofupp2001shep (coded sampling abundance 2000. 13.0 fish of during sites mouth) themiographs, from of (upstream locations kilometers showing stream drainage and River captured), Judith or Fork observed South upper species of fish Map by 1 . Figure