Fisheries Investigations in the Big Blackfoot River Basin Montana, 2013-2015 By Ron Pierce and Craig Podner Fisheries Investigations in the Big Blackfoot River Basin Montana, 2013-2015 by Ron Pierce and Craig Podner Montana Fish, Wildlife and Parks 3201 Spurgin Road Missoula, MT 59804 May 2016 1 TABLE OF CONTENTS INTRODUCTION………………………………………………………………... 4 EXECUTIVE SUMMARY……………………………………………………… 5 STUDY AREA……………………………………………………………………. 8 PROCEDURES Fish Population Estimators………………………………………………… 12 Stream Temperature………………………………………………..………. 15 Working with Private Landowners……………………………………….... 16 RESULTS/DISCUSSION PART I: Blackfoot River Environment Blackfoot River Discharge………………………………………………… 17 Blackfoot River and Tributary Temperatures……………… ……………... 17 PART II: Blackfoot River Trout Population surveys 1988-2014……………… 18 Blackfoot River Survey Sections...............................………………........... 18 Mountain whitefish surveys.......................................................................... 22 Bull Trout Conservation…………………………………………………… 24 PART III: Tributary Restoration and Fisheries Monitoring.............................. 28 Ashby Creek……………………………………………………………….. 28 Bear Creek…………………………………………………………………. 29 Belmont Creek…………………………………………………………….. 30 Braziel Creek………………………………………………………………. 31 Chamberlain Creek………………………………………………………… 32 Copper Creek………………………………………………………………. 33 Cottonwood Creek………………………………………………………… 34 Enders Spring Creek ……………………………………………………... 36 Gold Creek………………………………………………………………… 37 Grantier Spring Creek.................................................................................... 38 Jacobsen Spring Creek……………………………………………………... 39 Keep Cool Drainage……………………………………………………….. 40 Keep Cool Creek…………………………………………………… 41 Sucker Creek..................................................................................... 43 Liverpool Creek................................................................................ 43 Stonewall Creek................................................................................ 44 Park Creek......................................................................................... 46 Beaver Creek..................................................................................... 47 Theodore, Klondike and Yukon Creeks........................................... 48 Lincoln Spring Creek........................................................................ 49 Monture Creek……………………………………………………………... 50 Murphy Spring Creek…………………………………………………….... 51 Nevada Creek................................................................................................ 52 North Fork of the Blackfoot River………………………………………… 55 Pearson Creek……………………………………………………………… 57 2 PART III: Tributary Restoration and Fisheries Monitoring (cont.) Poorman Creek…………………………………………………………….. 58 Sauerkraut Creek........................................................................................... 59 Shanley Creek……………………………………………………………… 60 Snowbank Creek…………………………………………………………… 61 Wasson Creek……………………………………………………………… 62 RECOMMENDATIONS........................................................................................ 64 LITERATURE CITED.......................................................................................... 65 ACKNOWLEDGEMENTS................................................................................... 68 PART IV: Special Studies………………………………………………………... 69 1. Final Report: Westslope cutthroat trout movements through restored habitat and Coanda diversions in the Nevada Spring Creek complex, Blackfoot Basin, Montana.........................................................................TAFS 143:230-239, 2014. 2. Final Report: Instream habitat restoration and stream temperature reduction in a whirling disease-positive spring creek in the Blackfoot River Basin, Montana......................................................................TAFS 143:1188-1198, 2014. 3. Final Report: Long-term increases in trout abundance following channel reconstruction, instream wood placement, and livestock removal from a spring creek in the Blackfoot Basin, Montana………………..TAFS 144:184-195, 2015. 4. Draft Report: Channel form, spawning site quality and benthic invertebrates in small restored spring creeks of western Montana...........................................1-16. 5. Final Report: Does whirling disease mediate hybridization between a native and nonnative trout?..........................................NAJFM 35:337-351, 2015. 6. Final report: Multiscale prediction of whirling disease risk in the Blackfoot River Basin, Montana: a useful consideration for restoration Prioritization?................... …………………………………………………………TAFS 144:753-766, 2015. 7. Draft Report: Genetic assignment of bull trout in the Clearwater Basin Lakes and Blackfoot River to natal tributaries………………………………………………...1-9. APPENDICES Appendix A: Summary of catch and size statistics for Blackfoot tributaries, 2013-2015. Appendix B: Summary of two-pass estimates for tributaries, 2013-2015. Appendix C: Mark and recapture estimates, 2013-2015. Appendix D: Summary of water chemistry readings, 2013-2015. Appendix E: Summary of water temperatures, 2013-2015. Appendix F: Genetic test results for westslope cutthroat trout, 2013-2015. Appendix G: Restoration streams and tables of activities. Appendix H: Potential restoration projects. Appendix I: Table of restoration streams and cooperators. 3 INTRODUCTION The Blackfoot Basin has been the site of a wild trout restoration initiative since 1988-89 when fisheries assessments first identified: 1) the over-harvest of native trout, 2) basin-scale degradation of riparian and aquatic habitat in tributaries, and 3) a long history of toxic mine waste in the headwaters of the Blackfoot River as limiting Blackfoot River fisheries (Peters and Spoon 1988; Peters 1990; Moore et al. 1991). These findings triggered basin-wide protective fishing regulations in 1990 followed by pilot-level restoration actions in tributaries of the Blackfoot River. By the mid-1990s, improved fisheries and social acceptance of the restoration initiative led to the refinement of a private lands restoration methodology for the Blackfoot River and the expansion of tributary restoration from the 1990s to the present (Aitkin 1997; Pierce et al. 1997, 2005, 2011, 2013; BBCTU 2016). While aquatic habitat improvement provides the foundation for this endeavor, the cooperation of many resource agencies, conservation groups, private landowners form the social and technical network necessary to focus, fund and implement the restoration work. This initiative provides a specific framework for the recovery of dwindling stocks of imperiled native trout when integrated with protective angling regulations, site-specific restoration and landscape protection (e.g., conservation easements) in ecologically critical areas of the watershed. Blackfoot River restoration is a voluntary, tributary-based, priority-driven process whereby the scope and scale of restoration expands as information and stakeholder cooperation is generated (Pierce et al. 2005, 2013). As an iterative process, restoration usually begins with fisheries and habitat assessments with emphasis on human-induced limiting factors, which then lead to restoration activities targeting individual tributary stocks. Restoration priorities focus on tributaries supporting migratory native trout and emphasize restoration techniques that include enhancing flows in rearing areas, preventing juvenile fish loss to irrigation in migration corridors, reconstructing damaged streams, fencing livestock from spawning areas, while expanding these types of actions to adjacent tributaries as limiting factors are identified and as opportunities allow. Within this restoration process, monitoring and project evaluations are critical to identify measures of biological effectiveness, as well as areas where adaptive management is required. After 28 years of fisheries field work, Montana Fish, Wildlife and Parks (FWP) has completed fisheries and/or habitat-related surveys on all major tributaries (n=207) within the Blackfoot River Basin, including 180 streams outside of designated wilderness/roadless areas. Of these 180 streams, fisheries investigations have identified human-induced fisheries impairments on >80% of inventoried streams (Pierce et al. 2008, Appendix H). With this and other fisheries information, and with the cooperation of many stakeholders, restoration has now targeted 78 tributaries with >500 individual fisheries improvement projects (Pierce et al. 2008; BBCTU 2016; Appendix G). Restoration emphasizes private lands at the lower elevations of the basin; however, restoration is now expanding to industrial timberlands and public lands following the transfers of former Plum Creek Timber Company lands to conservation groups and to public ownerships. Of these 78 streams, twenty eight streams now are now approaching final restoration phases (Appendix G). In addition to habitat work, the upper North Fork Basin upstream of the North Fork Falls (within the Scapegoat Wilderness) is now being considered as a possible large-scale native trout recovery area (Pierce et al. 2016). 4 Unlike the habitat restoration on lower elevation streams, the North Fork project would replace hybrid trout with native westslope cutthroat trout and bull trout in pristine high elevation habitat highly suited to native trout. With this continued expansion of fisheries improvement work, river restoration has increasingly evolved