KOOTENAI RIVER RESIDENT FISH MITIGATION: WHITE STURGEON, BURBOT, NATIVE SALMONID MONITORING AND EVALUATION Annual Progress Report May 1, 2016 — April 31, 2017 BPA Project # 1988-065-00 Report covers work performed under BPA contract # 68393 IDFG Report Number 08-09 April 2018 This report was funded by the Bonneville Power Administration (BPA), U.S. Department of Energy, as part of BPA's program to protect, mitigate, and enhance fish and wildlife affected by the development and operation of hydroelectric facilities on the Columbia River and its tributaries. The views in this report are the author's and do not necessarily represent the views of BPA. This report should be cited as follows: Ross et al. 2018. Report for 05/01/2016 – 04/30/2017. TABLE OF CONTENTS Page CHAPTER 1: KOOTENAI STURGEON MONITORING AND EVALUATION ............................... 1 ABSTRACT ................................................................................................................................. 1 INTRODUCTION ........................................................................................................................2 OBJECTIVE ................................................................................................................................3 STUDY SITE ...............................................................................................................................3 METHODS ..................................................................................................................................3 Water levels, discharge, and river temperature manipulation ................................................... 3 Adult Kootenai Sturgeon Sampling ...........................................................................................4 Adult Kootenai Sturgeon Telemetry ..........................................................................................4 Substrate Enhancement Pilot Projects ..................................................................................... 5 Habitat Selection ......................................................................................................................5 Spawning Occurrence ..............................................................................................................6 Hatching Success ....................................................................................................................6 Juvenile Kootenai Sturgeon Sampling ...................................................................................... 7 RESULTS ...................................................................................................................................7 Water Levels, Discharge, and River Temperature .................................................................... 7 Adult Kootenai Sturgeon Sampling ...........................................................................................8 Adult Kootenai Sturgeon Telemetry ..........................................................................................8 Substrate Enhancement Pilot Projects ..................................................................................... 9 Spawning Occurrence ..............................................................................................................9 Hatching Success ....................................................................................................................9 Juvenile Kootenai Sturgeon Sampling ...................................................................................... 9 DISCUSSION............................................................................................................................10 RECOMMENDATIONS ............................................................................................................. 11 TABLES ....................................................................................................................................13 FIGURES ..................................................................................................................................20 CHAPTER 2: BURBOT MONITORING AND EVALUATION ..................................................... 35 ABSTRACT ...............................................................................................................................35 INTRODUCTION ......................................................................................................................36 GOAL ........................................................................................................................................37 OBJECTIVES ...........................................................................................................................37 STUDY AREA ...........................................................................................................................37 METHODS ................................................................................................................................38 Burbot Hoopnet Sampling ...................................................................................................... 38 Burbot Stocking ................................................................................................................... 38 Mainstem Hoopnet Sampling .............................................................................................. 38 Burbot Survival, Movement, and Habitat Use in Deep Creek, Idaho ....................................... 39 Potential Effects of Water Temperature on the Egg Hatching Success, Larval Development, and Larval Survival of Burbot ..................................................................... 39 Efficiency Estimate of Larval Light Traps................................................................................ 39 Burbot Survival Analysis ........................................................................................................ 40 Virtual Population Analysis ..................................................................................................... 41 RESULTS ................................................................................................................................. 41 i Burbot Hoopnet Sampling ...................................................................................................... 41 Burbot Survival, Movement, and Habitat Use in Deep Creek, Idaho ....................................... 43 Potential Effects of Water Temperature on the Egg Hatching Success, Larval Development, and Larval Survival of Burbot ..................................................................... 43 Efficiency Estimate of Larval Light Traps................................................................................ 43 Burbot Survival Analysis ........................................................................................................ 43 Virtual Population Analysis ..................................................................................................... 44 DISCUSSION............................................................................................................................45 RECOMMENDATIONS ............................................................................................................. 48 TABLES ....................................................................................................................................49 FIGURES ..................................................................................................................................53 CHAPTER 3: NATIVE SALMONID MONITORING AND EVALUATION .................................... 72 ABSTRACT ...............................................................................................................................72 INTRODUCTION ......................................................................................................................73 RESEARCH GOAL ................................................................................................................... 74 OBJECTIVES ...........................................................................................................................74 STUDY AREA ...........................................................................................................................75 METHODS ................................................................................................................................75 Fish Community Assessment ................................................................................................. 75 Abundance, Biomass, and Relative Weight ......................................................................... 75 Population Status ................................................................................................................... 76 Analysis Considerations ......................................................................................................... 77 RESULTS ................................................................................................................................. 77 Fish Community Assessment ................................................................................................. 77 Abundance, Biomass, and Relative Weight ......................................................................... 77 Abundance (CPUE) ......................................................................................................