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19-0530 Lower Clear Creek Floodplain and Stream Channel

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19-0530 Lower Clear Creek Floodplain and Stream Channel Refer to NMFS ECO#: WCRO-2019-01994 September 16, 2019 Richard J. Woodley Regional Resources Manager Bureau of USBR Mid-Pacific Regional Office 2800 Cottage Way Sacramento, California 95825-1898 Re: Endangered Species Act Section 7(a)(2) Biological Opinion, and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response, for the Lower Clear Creek Floodplain and Stream Channel Restoration project, Phase 3C Dear Mr. Woodley: Thank you for your letter of June 26, 2019, requesting 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 Lower Clear Creek Floodplain and Stream Channel Restoration Project, Phase 3C (Project), and for your follow up final/updated biological assessment on July 28, 2019. Based on the best available scientific and commercial information, the biological opinion concludes that the Project, is not likely to jeopardize the continued existence of the federally listed threatened Central Valley spring-run Chinook salmon evolutionarily significant unit (Oncorhynchus tshawytscha) or the threatened California Central Valley steelhead distinct population segment (O. mykiss), and is not likely to destroy or adversely modify their designated critical habitats. For the above species, NMFS has included an incidental take statement with reasonable and prudent measures and non-discretionary terms and conditions that are necessary and appropriate to avoid, minimize, or monitor incidental take of listed species associated with the project. NMFS reviewed the likely effects of the proposed action on essential fish habitat (EFH), pursuant to section 305(b) of the Magnuson-Stevens Fishery Conservation and Management Act (16 U.S.C. 1855(b)), and concluded that the action would adversely affect the EFH of Pacific Coast Salmon. Therefore, we have included the results of that review in Section 3 of this document. 2 Please contact Jahnava Duryea at the NMFS CCVO at (916) 930-3725 or via email at [email protected], if you have any questions concerning this Section 7 consultation, or if you require additional information. Enclosure cc: To the file 151422-WCR2019-SA00530 Mr. Doug Kleinsmith, Reclamation Natural Resources Specialist, [email protected] Mr. Sean Frische, Reclamation Clear Creek Phase 3C Project Manager, [email protected] Mr. Stephen Laymon Wildlife Biologist Redding Field Office Bureau of Land Management 6640 Lockheed Drive Redding, CA 96002 Mr. Guy Chetelat Engineering Geologist Central Valley Regional Water Quality Control Board 364 Knollcrest Drive, Suite 205 Redding, CA 96002 Endangered Species Act Section 7(a)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response Lower Clear Creek Floodplain and Stream Channel Restoration project, Phase 3C NMFS Consultation Number: WCRO-2019-01994 Action Agency: United States Bureau of Reclamation Affected Species and NMFS’ Determinations: Is Action Is Action Is Action Likely Is Action Likely ESA-Listed Likely to Likely To to Adversely To Destroy or Status Species Adversely Jeopardize Affect Critical Adversely Modify Affect Species? the Species? Habitat? Critical Habitat? Central Valley Threatened Yes No Yes No spring-run Chinook salmon (Oncorhynchus tshawytscha) California Central Threatened Yes No Yes No Valley steelhead (O. mykiss) Fishery Management Plan That Does Action Have an Are EFH Conservation Identifies EFH in the project Area Adverse Effect on EFH? Recommendations Provided? Pacific Coast Salmon Yes Yes Consultation Conducted By: National Marine Fisheries Service, West Coast Region Date: September 16, 2019 Table of Contents TABLE OF CONTENTS TABLE OF CONTENTS ................................................................................................................ ii LIST OF ACRONYMS ................................................................................................................. iv 1 INTRODUCTION .................................................................................................................. 1 1.1 Background ........................................................................................................................... 1 1.2 Consultation History ............................................................................................................. 1 1.3 Proposed Federal Action ....................................................................................................... 2 1.3.1 Project Location ............................................................................................................. 2 1.3.2 Project Description......................................................................................................... 3 1.3.3 Avoidance and Minimization Measures ...................................................................... 12 2 ENDANGERED SPECIES ACT: ........................................................................................ 17 2.1 Analytical Approach ........................................................................................................... 17 2.2 Range wide Status of the Species and Critical Habitat ....................................................... 18 2.2.1 Central Valley Spring-run Chinook Salmon ................................................................ 19 2.2.2 California Central Valley Steelhead ............................................................................ 31 2.2.3 Climate Change ............................................................................................................ 39 2.3 Action Area ......................................................................................................................... 41 2.4 Environmental Baseline ...................................................................................................... 41 2.4.1 Status of Species and Critical Habitat in the Action Area ........................................... 44 2.4.2 Factors Affecting Species and Critical Habitat in Clear Creek ................................... 47 2.4.3 Conclusion: Likelihood of Species Survival and Recovery in the Action Area .......... 48 2.5 Effects of the Action ........................................................................................................... 49 2.5.1 Construction Impact Analysis ...................................................................................... 50 2.5.2 Effects of the Proposed Action to Critical Habitat and PBFs ...................................... 54 2.6 Cumulative Effects.............................................................................................................. 57 2.6.1 Habitat Restoration ...................................................................................................... 57 2.6.2 Agricultural Practices ................................................................................................... 57 2.6.3 Mining Activities ......................................................................................................... 58 2.6.4 Urban Development ..................................................................................................... 58 2.7 Integration and Synthesis .................................................................................................... 59 2.7.1 Summary of the Status of the Species and Critical Habitat ......................................... 59 2.7.2 Effects of the Action to Listed Species and the Environmental Baseline .................... 64 2.7.3 Aggregate analysis for the ESU/DPS as a whole......................................................... 65 2.7.4 Summary of Effects of the Action on Critical Habitat ................................................ 66 NMFS Biological Opinion for the ii September 16, 2019 Lower Clear Creek Floodplain and Stream Channel Restoration project, Phase 3C Table of Contents 2.8 Conclusion .......................................................................................................................... 66 2.9 Incidental Take Statement................................................................................................... 66 2.9.1 Amount or Extent of Take ........................................................................................... 66 2.9.2 Effect of the Take......................................................................................................... 68 2.9.3 Reasonable and Prudent Measures ............................................................................... 68 2.9.4 Terms and Conditions .................................................................................................. 68 2.10 Conservation Recommendations ...................................................................................... 70 2.11 Reinitiation of Consultation .............................................................................................. 70 3 MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT ESSENTIAL FISH HABITAT RESPONSE ................................................................................ 71 3.1 Essential Fish Habitat Affected by the Project ................................................................... 71 3.2 Adverse Effects on Essential Fish Habitat .......................................................................... 71 3.2.1 Sedimentation and Turbidity.......................................................................................
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