ENDANGERED SPECIES AND ESSENTIAL FISH HABITAT BIOLOGICAL ASSESSMENT Port of San Francisco Regional General Permit for Shoreline Maintenance Repair, Rehabilitation, and Replacement Activities National Marine Fisheries Service April 2015 ENDANGERED SPECIES AND ESSENTIAL FISH HABITAT BIOLOGICAL ASSESSMENT Port of San Francisco Regional General Permit for Shoreline Maintenance Repair, Rehabilitation, and Replacement Activities National Marine Fisheries Service April 2015 Prepared for: The Port of San Francisco Prepared by: Environmental Science Associates 550 Kearny Street, Suite 800 San Francisco, CA 94108 TABLE OF CONTENTS Endangered Species and Essential Fish Habitat Biological Assessment Page Glossary and Acronyms ............................................................................................................................ v Glossary ................................................................................................................................................. v Acronyms ............................................................................................................................................. vi 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 Proposed Species and Habitat covered in this Biological Assessment .............................................................................................................. 1‐4 1.3.1 ESA Protected Species ................................................................................................... 1‐4 1.3.2 Federal Candidate and CESA Protected Species ....................................................... 1‐5 1.3.3 Critical Habitat ............................................................................................................... 1‐5 1.3.4 Essential Fish Habitat .................................................................................................... 1‐5 1.3.5 MMPA Protected Species ............................................................................................. 1‐6 1.3.6 Habitat Areas of Particular Concern (HAPC) ............................................................ 1‐6 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 ................................. 4‐6 4.3.2 Removal of Dilapidated Structures and Support Piles ........................................... 4‐10 4.4 Construction Equipment and Methods ............................................................................... 4‐11 4.5 Schedule ................................................................................................................................... 4‐12 5. Avoidance, Minimization, and Conservation Measures ........................................................... 5‐1 6. Species Accounts .............................................................................................................................. 6‐1 6.1 ESA List of Species ................................................................................................................... 6‐1 6.1.1 Green Sturgeon‐Southern DPS (Acipenser medirostris) .............................................. 6‐1 6.1.2 Steelhead (Oncorhynchus mykiss), Central California Coast ESU ............................ 6‐2 6.1.3 Steelhead (Oncorhynchus mykiss), California Central Valley ESU ........................... 6‐6 6.1.4 Chinook Salmon, Sacramento winter‐run (Oncorhynchus tshawytscha) .................. 6‐7 Port of San Francisco RGP for Shoreline Maintenance i April 2015 Biological Assessment Table of Contents Page 6. Species Accounts (continued) 6.1.5 Chinook Salmon, Central Valley (Sacramento) spring‐run (Oncorhynchus tshawytscha) ..................................................................................................................... 6‐9 6.2 Federal Candidate/CESA Listed Species ............................................................................. 6‐10 6.2.1 Longfin Smelt (Spirinchus thaleichthys) ...................................................................... 6‐10 6.3 EFH Species ............................................................................................................................. 6‐11 6.4 Habitats of Particular Concern (HAPC) .............................................................................. 6‐13 6.4.1 Eelgrass (Zostera marina) Beds .................................................................................... 6‐13 6.4.2 Native Olympia oysters (Ostrea lurida) Beds ............................................................ 6‐14 7. Environmental Baseline .................................................................................................................. 7‐1 7.1 Water Quality ............................................................................................................................ 7‐1 7.2 Sediment Quality ...................................................................................................................... 7‐3 7.3 Marine Habitats ........................................................................................................................ 7‐4 7.3.1 Open Water (Pelagic) Habitat ...................................................................................... 7‐4 7.3.2 Intertidal and Subtidal Habitats .................................................................................. 7‐5 7.4 Non‐native and Invasive Species ......................................................................................... 7‐11 8. Effects of the Action ......................................................................................................................... 8‐1 8.1 Effects from In‐water Maintenance Activities ...................................................................... 8‐1 8.1.1 Water /Sediment Quality Effects ................................................................................. 8‐1 8.1.2 Noise Effects from Pile Driving ................................................................................... 8‐3 8.2 Effects to Wetlands and Special Aquatic Sites ...................................................................... 8‐6 8.3 Cumulative Effects (Future State, Tribal, Local, and Private Actions) .............................. 8‐7 9. Conclusion and Determination ..................................................................................................... 9‐1 9.1 ESA Section 7 ............................................................................................................................ 9‐1 9.1.1 Water Quality Impairment ........................................................................................... 9‐1 9.1.2 Noise ................................................................................................................................ 9‐1 9.2 Magnuson‐Stevens Fishery Conservation and Management Act (Essential Fish Habitat) ............................................................................................................ 9‐2 10. References ........................................................................................................................................ 10‐1 Appendices A. Special‐Status Fish and Marine Mammal Species that May Occur Within the Bay Waters of the Proposed Project ........................................................................................... A‐1 B. U.S. Fish and Wildlife Service Species Lists ................................................................................... B‐1 C. CDFW Fish Data for Central Bay for Years 2005 Through 2009 ................................................. C‐1 List of Figures Figure 1 Vicinity Map .......................................................................................................................... 1‐2 Figure 2 Port of S.F. Jurisdiction ......................................................................................................... 1‐3 Figure 2a Action Area ...........................................................................................................................