BIOLOGICAL EVALUATION SKAGIT RIVER HYDROELECTRIC PROJECT LICENSE (FERC NO. 553) AMENDMENT: ADDITION OF A SECOND POWER TUNNEL AT THE GORGE DEVELOPMENT Final June 2011 BIOLOGICAL EVALUATION Table of Contents 1 INTRODUCTION .................................................................................................................. 1 1.1. Project Location .........................................................................................................2 1.2. Summary of Skagit River Project History ..................................................................2 1.2.1. Project Construction and Original License ................................................... 2 1.2.2. Settlement Agreement and Current License .................................................. 2 2 EXISTING PROJECT FACILITIES, OPERATIONS, AND MITIGATION AND CONSERVATION MEASURES ........................................................................................... 6 2.1. Existing Project Facilities ...........................................................................................6 2.1.1. Project Developments ................................................................................... 6 2.1.2. Diablo and Newhalem ................................................................................... 7 2.1.3. Project Transmission Lines ........................................................................... 7 2.2. Existing Operations – Reservoirs ...............................................................................8 2.2.1. Ross Lake ...................................................................................................... 8 2.2.2. Diablo Lake ................................................................................................... 8 2.2.3. Gorge Lake .................................................................................................... 9 2.3. Existing Operations – Downstream Flows .................................................................9 2.3.1. Salmon Spawning and Redd Protection ........................................................ 9 2.3.2. Salmon Fry Protection ................................................................................. 10 2.3.3. Steelhead Spawning and Redd Protection ................................................... 11 2.3.4. Steelhead Fry Protection ............................................................................. 11 2.3.5. Other Flow Management Measures ............................................................ 12 2.4. Existing Mitigation Measures ..................................................................................13 2.4.1. FSA Non-Flow Plan Measures .................................................................... 13 2.4.2. Wildlife Mitigation Measures ..................................................................... 16 2.5. Existing Conservation Measures for ESA-Listed Fish ............................................20 2.5.1. EAP Habitat Acquisition Projects ............................................................... 21 2.5.2. EAP Habitat Restoration Projects ............................................................... 21 2.5.3. EAP Research Projects ................................................................................ 21 3 PROPOSED ACTION .......................................................................................................... 27 3.1. Proposed New Facilities ...........................................................................................27 3.2. Proposed Project Operations as Amended ...............................................................33 3.3. Proposed Conservation Measures ............................................................................34 3.3.1. Additional Flow Measures .......................................................................... 34 3.3.2. Listed Fish Species Recovery Measures ..................................................... 35 3.4. Federal Action History Related to the Proposed Action ..........................................38 Skagit Hydroelectric Project Seattle City Light FERC No. 553 ii June 2011 BIOLOGICAL EVALUATION 4 ACTION AREA .................................................................................................................... 40 4.1. Aquatic Action Area .................................................................................................40 4.2. Terrestrial Action Area .............................................................................................40 4.3. Known Ongoing and Previous Federal Actions within the Action Area .................40 4.3.1. Skagit Basin Comprehensive Flood Hazard Management Plan (FEMA Authority) .................................................................................................... 41 4.3.2. Corp of Engineers Flood Control ................................................................ 41 4.3.3. Baker River Hydroelectric Project Relicensing .......................................... 42 5 LISTED SPECIES, RANGEWIDE STATUS, AND CRITICAL HABITAT ..................... 43 5.1. Species Description and Status ................................................................................43 5.1.1. Puget Sound Chinook Salmon ..................................................................... 43 5.1.2. Puget Sound Steelhead ................................................................................ 68 5.1.3. Bull Trout .................................................................................................... 72 5.1.4. Marbled Murrelet ........................................................................................ 84 5.1.5. Northern Spotted Owl ................................................................................. 86 5.1.6. Grizzly Bear ................................................................................................ 86 5.1.7. Gray Wolf .................................................................................................... 87 5.1.8. Canada Lynx ............................................................................................... 88 5.2. Critical Habitat Designations ...................................................................................88 5.2.1. Chinook Salmon .......................................................................................... 88 5.2.2. Steelhead ..................................................................................................... 88 5.2.3. Bull Trout .................................................................................................... 89 5.2.4. Marbled Murrelet ........................................................................................ 89 5.2.5. Northern Spotted Owl ................................................................................. 89 5.2.6. Grizzly Bear ................................................................................................ 89 5.2.7. Gray Wolf .................................................................................................... 89 5.2.8. Canada Lynx ............................................................................................... 89 6 ENVIRONMENTAL BASELINE AND CUMULATIVE EFFECTS ................................. 96 6.1. Status of Habitat Features within the Aquatic Action Area .....................................96 6.1.1. Water Quality .............................................................................................. 96 6.1.2. General Status of Fish Habitat in the Skagit Basin ................................... 104 6.1.3. Puget Sound Chinook Salmon ................................................................... 127 6.1.4. Puget Sound Steelhead .............................................................................. 128 6.1.5. Bull Trout .................................................................................................. 130 6.1.6. Cumulative Effects .................................................................................... 132 6.2. Status of Wildlife Habitat Features within the Terrestrial Action Area .................142 6.2.1. Marbled Murrelet ...................................................................................... 143 6.2.2. Northern Spotted Owl ............................................................................... 144 6.2.3. Grizzly Bear .............................................................................................. 145 6.2.4. Gray Wolf .................................................................................................. 145 Skagit Hydroelectric Project Seattle City Light FERC No. 553 iii June 2011 BIOLOGICAL EVALUATION 6.2.5. Canada Lynx ............................................................................................. 146 7 EFFECTS OF THE ACTION ............................................................................................. 147 7.1. Fish .........................................................................................................................147 7.1.1. Skagit Project Facilities as Amended ........................................................ 147 7.1.2. Skagit Operations as Amended ................................................................. 151 7.2. Wildlife ...................................................................................................................155 7.2.1. Gorge 2nd Tunnel .....................................................................................