Chief Joseph Hatchery Program Biological Assessment Action Agency: Bonneville Power Administration Prepared by S.H. Smith Fisheries Consulting, Inc. and Meridian Environmental, Inc. May 3, 2006 Chief Joseph Hatchery Program CONTENTS I. INTRODUCTION ................................................................................................1 A. FEDERAL ACTION AND LEGAL AUTHORITY ............................................2 B. PROJECT AND FEDERAL ACTION HISTORY...............................................2 Regional Perspective.............................................................................................2 Chief Joseph Hatchery Master Program ...............................................................3 C. PROJECT PURPOSE AND OBJECTIVES.........................................................4 II. DESCRIPTION OF THE PROPOSED PROJECT ..............................................4 A. HATCHERY PROGRAMS..................................................................................4 B. PROJECT FACILITIES.......................................................................................6 Chief Joseph Hatchery..........................................................................................7 Housing and Other Facilities ..............................................................................11 Acclimation Ponds..............................................................................................14 C. FACILITY CONSTRUCTION...........................................................................21 Chief Joseph Hatchery........................................................................................21 Housing and Other Facilities ..............................................................................22 Acclimation Ponds..............................................................................................22 D. FACILITY OPERATIONS.................................................................................23 Chief Joseph Hatchery........................................................................................23 Housing and Other Facilities ..............................................................................24 Acclimation Ponds..............................................................................................24 E. PROPOSED CONSERVATION MEASURES..................................................25 Facility Construction...........................................................................................25 Program Operations ............................................................................................26 F. PROGRAM MONITORING..............................................................................26 G. RELATION OF PROPOSED PROJECT TO OTHER FEDERAL ACTIONS .27 Okanogan Subbasin Planning .............................................................................27 Salmon and Steelhead Limiting Factors Assessment Watershed Resource Inventory 49: Okanogan Watershed.........................................................28 Biological Assessment and Management Plan: Mid-Columbia River Hatchery Program ....................................................................................................28 Upper Columbia Salmon Recovery Plan............................................................28 Upper Columbia Biological Strategy..................................................................29 Colville Tribes’ Anadromous Fish Management Plan .......................................29 Okanogan Summer/Fall and Spring Chinook Hatchery and Genetic Management Plans ...................................................................................29 H. PROJECT AREA AND ACTION AREA DEFINED ........................................30 Okanogan River ..................................................................................................30 Omak Creek ........................................................................................................31 Columbia River...................................................................................................31 May 3, 2006 Draft Biological Assessment - Page i Chief Joseph Hatchery Program III. STATUS OF SPECIES AND CRITICAL HABITAT .......................................32 A. SPECIES LISTS FROM THE SERVICES ........................................................32 Identification of Listed Species ESU/DPS .........................................................32 Identification of Designated and Proposed Critical Habitat ...............................33 B. USFWS-MANAGED SPECIES EXCLUDED FROM FURTHER ANALYSIS: PROPOSED ACTION IS "NOT LIKELY TO ADVERSELY AFFECT".........33 Gray Wolf ...........................................................................................................33 Bald Eagle...........................................................................................................34 Ute ladies’-tresses...............................................................................................35 Yellow-billed Cuckoo.........................................................................................36 Columbia River Bull Trout.................................................................................36 C. DESCRIPTION OF NOAA FISHERIES-MANAGED SPECIES TO BE ANALYZED FOR FORMAL CONSULTATION: PROPOSED ACTION IS "LIKELY TO ADVERSELY AFFECT"............................................................38 UCR Spring Chinook Salmon ............................................................................38 UCR Steelhead....................................................................................................40 IV. ENVIRONMENTAL BASELINE MATRIX.....................................................43 A. WATER QUALITY............................................................................................45 Water Temperature .............................................................................................45 Sediment/Turbidity .............................................................................................46 Chemical Contamination/Nutrients ....................................................................47 B. HABITAT ACCESS...........................................................................................47 Physical Barriers.................................................................................................47 C. HABITAT ELEMENTS.....................................................................................48 Substrate..............................................................................................................48 Large Woody Debris...........................................................................................48 Pool Frequency/Quality ......................................................................................48 Off-channel Habitat ............................................................................................49 Refugia................................................................................................................49 D. CHANNEL CONDITION/DYNAMICS............................................................49 Width/Depth Ratio..............................................................................................49 Streambank Condition ........................................................................................49 Floodplain Connectivity .....................................................................................50 E. FLOW/HYDROLOGY.......................................................................................50 Change in Peak/Base Flows................................................................................50 Increase in Drainage Network ............................................................................50 F. WATERSHED CONDITIONS...........................................................................51 Road Density and Location.................................................................................51 Disturbance History ............................................................................................51 Riparian Reserves ...............................................................................................51 V. EFFECTS OF THE ACTION.............................................................................52 A. DIRECT EFFECTS.............................................................................................52 May 3, 2006 Draft Biological Assessment - Page ii Chief Joseph Hatchery Program Construction Effects ...........................................................................................52 Operation Effects ................................................................................................55 B. INDIRECT EFFECTS........................................................................................60 Competition ........................................................................................................61 Straying...............................................................................................................62 Harvest................................................................................................................62 Salmon Carcass Deposition ................................................................................63 C. EFFECTS FROM INTERDEPENDENT AND INTERRELATED ACTIONS 63 D. DESCRIPTION OF HOW THE ENVIRONMENTAL BASELINE WOULD