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BIOLOGICAL ASSESSMENT Port of San Francisco Regional General Permit for Shoreline Maintenance Repair, Rehabilitation, and Replacement Activities

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BIOLOGICAL ASSESSMENT Port of San Francisco Regional General Permit for Shoreline Maintenance Repair, Rehabilitation, and Replacement Activities BIOLOGICAL ASSESSMENT Port of San Francisco Regional General Permit for Shoreline Maintenance Repair, Rehabilitation, and Replacement Activities U.S. Army Corps of Engineers and U.S. Fish and Wildlife Service April 2015 Prepared for: The Port of San Francisco BIOLOGICAL ASSESSMENT Port of San Francisco Regional General Permit for Shoreline Maintenance Repair, Rehabilitation, and Replacement Activities U.S. Army Corps of Engineers and U.S. Fish and Wildlife Service April 2015 Prepared for: The Port of San Francisco Prepared by: Environmental Science Associates (ESA) Brian Pittman 350 Frank H. Ogawa Plaza Suite 300 Oakland, CA 94612 510.839.5066 www.esassoc.com and Coast Ridge Ecology 1410 31st Avenue San Francisco, CA 94122 TABLE OF CONTENTS Biological Assessment Page 1. Introduction and Regulatory Authority ....................................................................................... 1‐1 1.1 U.S. Army Corps of Engineers Regulatory Authority ......................................................... 1‐4 1.2 Regulatory Requirements ........................................................................................................ 1‐4 1.3 Threatened, Endangered or Candidate Species covered in this Biological Assessment .... 1‐4 1.4 Critical Habitat .......................................................................................................................... 1‐5 2. Consultation ...................................................................................................................................... 2‐1 2.1 Consultation to Date ................................................................................................................ 2‐1 2.2 Future Consultation ................................................................................................................. 2‐2 3. Action Area ........................................................................................................................................ 3‐1 4. Project Description ........................................................................................................................... 4‐1 4.1 Background ............................................................................................................................... 4‐1 4.2 Project Purpose and Objectives .............................................................................................. 4‐2 4.3 Proposed Project Activities ..................................................................................................... 4‐5 4.3.1 Maintenance, Repair, and Restoration of Existing Structures ................................. 4‐5 4.3.2 Removal of Dilapidated Structures and Support Piles ........................................... 4‐10 4.4 Construction Equipment and Methods ............................................................................... 4‐11 4.5 Schedule ................................................................................................................................... 4‐11 5. Avoidance, Minimization, and Conservation Measures ........................................................... 5‐1 5.1 Avoidance and Minimization Measures ............................................................................... 5‐1 5.2 Conservation Measures ........................................................................................................... 5‐8 5.2.1 California Ridgway’s Rail (Clapper Rail) ................................................................... 5‐8 5.2.2 California Least Tern ..................................................................................................... 5‐9 5.2.3 Longfin Smelt ................................................................................................................. 5‐9 5.2.4 California Sea‐blite ........................................................................................................ 5‐9 6. Species Accounts and Status of the Species in the Action Area .............................................. 6‐1 6.1 California Ridgway’s Rail ........................................................................................................ 6‐1 6.2 California Least Tern ................................................................................................................ 6‐2 6.3 Longfin Smelt ............................................................................................................................ 6‐3 6.4 California Sea‐blite ................................................................................................................... 6‐4 7. Environmental Baseline .................................................................................................................. 7‐1 7.1 Land Use .................................................................................................................................... 7‐1 7.2 Hydrology ................................................................................................................................. 7‐1 7.3 Terrestrial Habitat .................................................................................................................... 7‐2 7.4 California Ridgway’s Rail, California Least Tern, Longfin Smelt and California Sea‐blite ................................................................................................................... 7‐3 Port of San Francisco RGP for Shoreline Maintenance i April 2015 Biological Assessment Table of Contents Page 8. Effects of the Action ......................................................................................................................... 8‐1 8.1 California Ridgway’s Rail ........................................................................................................ 8‐1 8.2 California Least Tern ................................................................................................................ 8‐2 8.3 Longfin Smelt ............................................................................................................................ 8‐2 8.4 California Sea‐blite ................................................................................................................... 8‐2 8.5 Critical Habitat Effects ............................................................................................................. 8‐3 8.6 Cumulative Effects (Future State, Tribal, Local, and Private Actions) .............................. 8‐3 9. Conclusion and Determination ..................................................................................................... 9‐1 10. References ........................................................................................................................................ 10‐1 Appendices 1. U.S. Fish and Wildlife Service Species Lists .................................................................................. A‐1 List of Figures Figure 1 Vicinity Map ........................................................................................................................ 1‐2 Figure 2 Port of S.F. Jurisdiction ....................................................................................................... 1‐3 Figure 2a Action Area .......................................................................................................................... 3‐2 Figure 3a Seawall Construction Types (Rock Embarkment & Wood Seawall and Concrete Seawall) ............................................................................................................ 4‐3 Figure 3b Seawall Construction Types (Exposed Rip Rap and Natural Shorelines) ................... 4‐4 List of Tables Table 4‐1 Proposed Activities – Estimated Areas and Volumes .................................................... 4‐6 Port of San Francisco RGP for Shoreline Maintenance ii April 2015 Biological Assessment CHAPTER 1 Introduction and Regulatory Authority The purpose of this Biological Assessment (BA) is to review the Port of San Francisco’s proposed project (federal action) in sufficient detail to determine to what extent the proposed maintenance repair, replacement, rehabilitation, and permanent removal actions may affect species listed as threatened, endangered or candidate species under the Federal Endangered Species Act (FESA), along with any designated or proposed critical habitats identified in the Action Area. It specifically evaluates the effects of potential federal actions necessary to permit the proposed project. The following information uses the best scientific and commercial information available when assessing the risks posed to listed and/or candidate species and designated and/or proposed critical habitat by federal actions. This BA has been prepared to address all of the potential ‘effects of the action’ (as defined in 50 CFR 402) on listed species that could be associated with the proposed project in accordance with Section 7 of the FESA and associated implementing regulations (50 CFR 402). This BA has been prepared to complete informal consultation with the U.S. Fish & Wildlife Service (USFWS) and will be used by the U.S. Army Corps of Engineers (Corps) and the Port of San Francisco to ensure their compliance with Section 7 of FESA for their permitting processes, as described below. In addition, a BA prepared for National Marine Fisheries Service (NMFS) and the California Department of Fish and Wildlife’s Marine Region (CDFW Marine) presents detailed information about the aquatic environment
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