Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat (EFH) Consultation
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Endangered Species Act (ESA) Section 7(a)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat (EFH) Consultation Leavenworth National Fish Hatchery Spring Chinook Salmon Program (Reinitiation 2016) NMFS Consultation Number: WCR-2017-7345 Action Agencies: United States Fish and Wildlife Service United States Bureau of Reclamation United States Environmental Protection Agency Affected Species and Determinations: ESA-Listed Species Status Is the Action Is the Action Is the Action Likely To Likely to Likely To Destroy or Adversely Adversely Affect Jeopardize the Modify Critical Species or Critical Species? Habitat? Habitat? Upper Columbia River Threatened Yes No No steelhead (Oncorhynchus mykiss) Upper Columbia River Endangered Yes No No spring-run Chinook salmon (O. tshawytscha) Fishery Management Plan That Does the Action Have an Adverse Are EFH Conservation Describes EFH in the Project Area Effect on EFH? Recommendations Provided? Pacific Coast Salmon Yes Yes I I I I Consultation Conducted By: National Marine Fisheries Service, West Coast Region Issued By: fbe_ _________________________ ff!).Barry A. Thom Regional Administrator West Coast Region Date: 9/29/2017 This page intentionally left blank. ii TABLE OF CONTENTS 1. INTRODUCTION ........................................................................................................................ 1 1.1. Background ..................................................................................................................... 1 1.2. Consultation History ....................................................................................................... 1 1.3. Proposed Action .............................................................................................................. 9 1.4. Action Area ................................................................................................................... 27 2. ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND INCIDENTAL TAKE STATEMENT ..... 30 2.1. Analytical Approach--Overview ................................................................................... 30 2.2. Range-wide Status of the Species and Critical Habitat ................................................ 33 2.2.1, Status of Listed Species .......................................................................................... 33 2.2.1.1. Life History and Status of UCR Chinook Salmon .......................................... 34 2.2. 1.2. Life History and Status of UCR Steelhead ...................................................... 38 2.2.2. Status of Critical Habitat ......................................................................................... 46 2,2,2,1. Critical Habitat for Upper Columbia River Spring Chinook Salmon ............. 48 2.2.2.2. Critical Habitat for Upper Columbia River Steelhead ..................................... 50 2.2.3. Climate Change ....................................................................................................... 53 2.3. Environmental Baseline ................................................................................................ 55 2.3.1. Land Ownership ...................................................................................................... 56 2.3.2. Resource Development ........................................................................................... 56 2.3.3. Restoration .............................................................................................................. 61 2.3.4. Hatchery Propagation.............................................................................................. 64 2.3.5. Fisheries .................................................................................................................. 73 2.3.6. Research, Monitoring, and Evaluation (RM&E) .................................................... 75 2.3.7. Climate Change ....................................................................................................... 75 2.4. Effects of the Action on ESA Protected Species and on Designated Critical Habitat .. 76 2.4. I. Factors Considered When Analyzing Hatchery Effects ......................................... 76 2.4.1.1. Factor 1. The hatchery program does or does not remove fish from the natural population and use them for hatchery broodstock ............................................................ 80 2.4. I .2. Factor 2. Hatchery fish and the progeny of naturally spawning hatchery fish on spawning grounds and encounters with natural-origin and hatchery fish at adult collection facilities 80 2.4. I .2.1. Genetic effects ......................................................................................... 81 2.4. I .2.2. Ecological effects .................................................................................... 88 2.4.1.2.3. Adult Collection Facilities ...................................................................... 89 iii 2.4.1.3. Factor 3. Hatchery fish and the progeny of naturally spawning hatchery fish in juvenile rearing areas ........................................................................................................ 89 2.4. 1.3.1. Competition ............................................................................................. 89 2.4. 1.3.2. Predation.................................................................................................. 91 2.4.1.3.3. Disease .................................................................................................... 93 2.4.1 .3.4. Acclimation ............................................................................................. 94 2.4. 1.4. Factor 4. Hatchery fish and the progeny of naturally spawning hatchery fish in the migration corridor, in the estuary, and in the ocean .................................................... 95 2.4. 1.5. Factor 5. Research, monitoring, and evaluation that exists because of the hatchery program .............................................................................................................. 96 2.4. 1.5, 1. Observing/disturbing ............................................................................... 96 2.4. 1.5.2. Capturing/handling .................................................................................. 96 2.4.1.5.3. Fin clipping and tagging .......................................................................... 97 2.4. 1.6. Factor 6. Construction, operation, and maintenance, of facilities that exist because of the hatchery program ...................................................................................... 97 2.4. 1.7. Factor 7. Fisheries that exist because of the hatchery program ....................... 97 2.4.2. Effects of the Proposed Action ............................................................................... 98 2.4.2.1. Factor 1. The hatchery program does or does not remove fish from the natural population and use them for hatchery broodstock .......................................................... 108 2.4.2.2. Factor 2. Hatchery fish and the progeny of naturally spawning hatchery fish on spawning grounds and encounters with natural-origin and hatchery fish at adult collection facilities 108 2.4.2.2. 1, Genetic effects ....................................................................................... 108 2.4.2.2.2. Ecological effects .................................................................................. 113 2.4.2.2.3. Broodstock Collection Facility Effects ................................................. 114 2.4.2.3. Factor 3. Hatchery fish and the progeny of naturally spawning hatchery fish in juvenile rearing areas ...................................................................................................... 117 2.4.2.4. Factor 4. Hatchery fish and the progeny of naturally spawning hatchery fish in the migration corridor, estuary, and ocean ...................................................................... 122 2.4.2.5. Factor 5. Research, monitoring, and evaluation that exists because of the hatchery program ............................................................................................................ 124 2.4.2.6. Factor 6. Construction, operation, and maintenance of facilities that exist because of the hatchery programs ................................................................................... 125 2.4.2.6.1. Physical effects of the LNFH instream structures on spring Chinook salmon and steelhead .................................................................................................. 128 2.4.2.6.2. Effects on freshwater spawning, rearing, and migration areas from the LNFH instream structures on spring Chinook salmon and steelhead ......................... 153 2.4.2.7. Factor 7. Fisheries that exist because of the hatchery program ..................... 173 iv 2.4.2.8. Effects of the Action Under Climate Change ................................................ 174 2.4.2.8.1. Climate Change Effects for the Upper Columbia River Watershed ..... 175 2.4.2.8.2. Climate Change Effects for Icicle Creek Watershed ............................ 178 2.4.2.8.3. Summary of Climate Change Effects .................................................... 183 2.4.2.9. Effects of the Action on Critical Habitat ....................................................... 184 2.4.2.9.1. UCR Spring Chinook Salmon ............................................................... 184 2.4.2.9.2. UCR Steelhead