KOOTENAI RIVER RESIDENT FISH MITIGATION: WHITE STURGEON, BURBOT, NATIVE SALMONID MONITORING AND EVALUATION Annual Progress Report May 1, 2017 – April 30, 2019 BPA Project # 1988-065-00 Report covers work performed under BPA contract # 75805 and 78985 IDFG Report Number 20-11 June 2020 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: Hardy et al. 2020. Report for 5/1/2017 - 4/30/2019. Annual Report, 1988-065-00. 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 ..........................................................................................5 Substrate Enhancement Pilot Projects ..................................................................................... 5 Spawning Occurrence ..............................................................................................................6 Larval Production .....................................................................................................................7 Juvenile Kootenai Sturgeon Sampling ...................................................................................... 7 Juvenile Hatchery Kootenai Sturgeon Age-1 Survival and Total Abundance ............................ 8 Juvenile Hatchery Kootenai Sturgeon Growth .......................................................................... 8 RESULTS ...................................................................................................................................9 Water Levels, Discharge, and River Temperature .................................................................... 9 Adult Kootenai Sturgeon Sampling ...........................................................................................9 Adult Kootenai Sturgeon Telemetry ........................................................................................ 10 Substrate Enhancement Pilot Projects ................................................................................... 10 Spawning Occurrence ............................................................................................................ 10 Hatching Success .................................................................................................................. 11 Juvenile Kootenai Sturgeon Sampling .................................................................................... 11 Juvenile Hatchery Kootenai Sturgeon Age-1 Survival and Total Abundance .......................... 11 Juvenile Hatchery Kootenai Sturgeon Growth ........................................................................ 12 DISCUSSION............................................................................................................................12 RECOMMENDATIONS ............................................................................................................. 14 TABLES ....................................................................................................................................15 FIGURES ..................................................................................................................................24 CHAPTER 2: EVALUATING THE UPSTREAM EXTENT OF SPAWNING MIGRATIONS OF KOOTENAI RIVER WHITE STURGEON....................................................................... 45 ABSTRACT ...............................................................................................................................45 INTRODUCTION ......................................................................................................................46 OBJECTIVES ...........................................................................................................................47 STUDY AREA ...........................................................................................................................47 METHODS ................................................................................................................................48 Libby Dam Operations ........................................................................................................... 48 Adult Sampling and Tagging .................................................................................................. 48 Acoustic Array ........................................................................................................................49 Analysis ................................................................................................................................. 49 RESULTS ................................................................................................................................. 50 i DISCUSSION............................................................................................................................51 TABLES ....................................................................................................................................53 FIGURES ..................................................................................................................................58 CHAPTER 3: WILD ADULT KOOTENAI RIVER WHITE STURGEON POPULATION UPDATE .............................................................................................................................64 ABSTRACT ...............................................................................................................................64 INTRODUCTION ......................................................................................................................65 OBJECTIVE ..............................................................................................................................65 STUDY SITE .............................................................................................................................65 METHODS ................................................................................................................................66 Adult Kootenai Sturgeon Sampling ......................................................................................... 66 Adult Kootenai Sturgeon Population Modeling ....................................................................... 66 RESULTS ................................................................................................................................. 66 DISCUSSION............................................................................................................................66 RECOMMENDATIONS ............................................................................................................. 67 FIGURES ..................................................................................................................................68 CHAPTER 4: BURBOT MONITORING AND EVALUATION ..................................................... 73 ABSTRACT ...............................................................................................................................73 INTRODUCTION ......................................................................................................................74 GOAL ........................................................................................................................................74 OBJECTIVES ...........................................................................................................................74 STUDY AREA ...........................................................................................................................75 METHODS ................................................................................................................................76 Burbot Hoopnet Sampling ...................................................................................................... 76 Burbot Stocking ...................................................................................................................76 Survival Analyses ................................................................................................................ 76 Mainstem Hoopnet Sampling .............................................................................................. 76 Tributary Use