Refer to NMFS No: WCR-2017-8532 August 31, 2018 Jennifer Steger Pacific Region Supervisor NOAA Restoration Center 777 Sonoma Avenue, Room 219-A Santa Rosa, California 95404 Nancy A. Haley Chief, California North Branch Regulatory Division U.S. Army Corps of Engineers 1325 J Street Sacramento, California 95814 Donald Ratcliff Central Valley Supervisor, Fish and Aquatic Conservation Pacific Southwest Region U.S. Fish and Wildlife Service 2800 Cottage Way Sacramento, California 95825 Re: Endangered Species Act Section 7(a)(2) Biological Opinion, and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response and Fish and Wildlife Coordination Act Recommendations for the NOAA Restoration Center’s Program to Facilitate Implementation of Restoration Projects in the Central Valley of California Dear Ms. Steger, Ms. Haley, and Mr. Ratcliff: Thank you for your letter of November 7, 2017, and subsequent information received on April 20, 2018, where you requested initiation of consultation with NOAA’s National Marine Fisheries Service (NMFS) pursuant to section 7 of the Endangered Species Act of 1973 (ESA) (16 U.S.C. 1531 et seq.) for the NOAA Restoration Center’s Program to Facilitate Implementation of Restoration Projects in the Central Valley of California. Thank you, also, for your request for consultation pursuant to the essential fish habitat (EFH) provisions in Section 305(b) of the Magnuson-Stevens Fishery Conservation and Management Act (MSA) (16 U.S.C. 1855(b)) for this action. 2 With this letter, we provide to you NMFS’s biological opinion (opinion) and EFH consultation based on our review of the NOAA Restoration Center’s Program to Facilitate Implementation of Restoration Projects in the Central Valley of California. The opinion analyzes the effects of the proposed action on endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha), threatened Central Valley spring-run Chinook salmon (O. tshawytscha), threatened California Central Valley steelhead (O. mykiss), threatened Southern Distinct Population Segment (sDPS) of North American green sturgeon (Acipenser medirostris), and their designated critical habitats per section 7 of the ESA. From our analysis NMFS concludes that the proposed action is not likely to jeopardize the continued existence of Sacramento River winter-run Chinook salmon, threatened Central Valley spring-run Chinook salmon, threatened California Central Valley steelhead, threatened sDPS green sturgeon, or adversely modify or destroy designated critical habitats for listed fish. Additionally, NMFS has included an incidental take statement with reasonable and prudent measures (RPM) and non-discretionary terms and conditions that are necessary and appropriate to avoid, minimize, or monitor incidental take of these listed species. NMFS also concludes that the proposed action will have minimal adverse effects to Pacific salmon, and Pacific groundfish EFH. Section 305(b)(2) of the MSA authorizes NMFS to provide EFH conservation recommendations to minimize adverse effects of an activity on EFH. Because any adverse effects to EFH will be minimal and multiple benefits to these habitats are expected, EFH conservation recommendations are not offered beyond what’s been considered in the terms and conditions of the RPM. However, if the proposed action is modified in a manner that may adversely affect EFH, the NOAA Restoration Center, U.S. Army Corps of Engineers and U.S. Fish and Wildlife Service will need to reinitiate EFH consultation with NMFS. Please contact Evan Sawyer ([email protected]) at the NMFS California Central Valley Office, (916) 930-3656, if you have any questions concerning this consultation, or if you require additional information. Sincerely, Enclosure cc: To the File 51422-WCR2017-SA00386 Endangered Species Act Section 7(a)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response and Fish and Wildlife Coordination Act Recommendations. NOAA Restoration Center’s Program to Facilitate Implementation of Restoration Projects in the Central Valley of California NMFS Consultation Number: WCR-2017-8532 Action Agencies: NOAA Restoration Center, the U.S. Army Corps of Engineers, and the United States Fish and Wildlife Service Affected Species and NMFS’ Determinations: ESA-Listed Status Is Action Is Action Is Action Is Action Species Likely to Likely to Likely to Likely to Adversely Jeopardize Adversely Destroy or Affect the Species? Affect Adversely Species? Critical Modify Critical Habitat? Habitat? Sacramento Endangered Yes No Yes No River winter-run Chinook salmon (Oncorhynchus tshawytscha) Central Valley Threatened Yes No Yes No spring-run Chinook salmon (O. tshawytscha) California Threatened Yes No Yes No Central Valley steelhead (O. mykiss) Southern Distinct Threatened Yes No Yes No Population Segment (sDPS) of North American green sturgeon (Acipenser medirostris) Affected Essential Fish Habitat and NMFS’ Determinations: Fishery Management Plan Does Action Have an Adverse Are EFH Conservation That Identifies EFH in the Effect on EFH? Recommendations Provided? Project Area Pacific Coast Salmon Yes No Pacific Ground Fish Yes No Consultation Conducted By: National Marine Fisheries Service, West Coast Region Issued By: Barry A. Thom Regional Administrator Date: August 31, 2018 NOAA Restoration Center’s Program to Facilitate Implementation of Restoration Projects in the Central Valley of California TABLE OF CONTENTS 1. INTRODUCTION .......................................................................................................................4 1.1 Background ....................................................................................................................... 4 1.2 Consultation History ......................................................................................................... 5 1.3 Proposed Federal Action ...................................................................................................... 7 1.3.1 Program Geographic Extent ............................................................................................. 8 1.3.2 Number of Anticipated Projects ....................................................................................... 8 1.3.3 Program Administration ................................................................................................... 9 1.3.4 Programmatic Sideboards and Other Program Requirements ........................................ 13 1.3.5 Covered Project Types and Prohibited Activities .......................................................... 17 1.3.6 Protection Measures ....................................................................................................... 31 1.3.7 Monitoring and Reporting Requirements ....................................................................... 42 2. ENDANGERED SPECIES ACT: .............................................................................................44 2.1 Analytical Approach ....................................................................................................... 45 2.2 Rangewide Status of the Species and Critical Habitat ................................................... 46 2.3 Action Area .................................................................................................................... 58 2.4 Environmental Baseline .................................................................................................. 59 2.4.1 Status of the Species in the Action Area ........................................................................ 59 2.5 Effects of the Action ....................................................................................................... 72 2.6 Cumulative Effects ......................................................................................................... 85 2.7 Integration and Synthesis ............................................................................................... 88 2.7.1 Cumulative Effects .......................................................................................................... 88 2.8 Conclusion ...................................................................................................................... 93 2.9 Incidental Take Statement .............................................................................................. 93 2.9.1 Amount or Extent of Take............................................................................................... 94 2.9.2 Effect of the Take ........................................................................................................... 95 2.9.3 Reasonable and Prudent Measures .................................................................................. 95 2.9.4 Terms and Conditions ..................................................................................................... 96 2.10 Conservation Recommendations .................................................................................... 98 2.11 Reinitiation of Consultation ........................................................................................... 98 3. MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT ESSENTIAL FISH HABITAT RESPONSE ..........................................................................98 3.1 Essential Fish Habitat Affected by the Project ............................................................... 99 3.2 Adverse Effects on Essential Fish Habitat ....................................................................