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Programmatic Essential Fish Habitat (EFH) Assessment for the Long-Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region
Programmatic Essential Fish Habitat (EFH) Assessment for the Long-Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region July 2009 Executive Summary Programmatic Essential Fish Habitat (EFH) Assessment for the Long-Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region Pursuant to section 305(b)(2) of the Magnuson-Stevens Fishery Conservation and Management Act of 1976 (16 U.S.C. §1855(b)), the United States Army Corps of Engineers (USACE) and the United States Environmental Protection Agency (USEPA), as the federal lead and co-lead agencies, respectively, submit this Programmatic Essential Fish Habitat (EFH) Assessment for the Long-Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region. This document provides an assessment of the potential effects of the on-going dredging and dredged material placement activities of all federal and non-federal maintenance dredging projects in the action area (see Figure 1.1 located on page 3). The SF Bay LTMS program area spans 11 counties, including: Marin, Sonoma, Napa, Solano, Sacramento, San Joaquin, Contra Costa, Alameda, Santa Clara, San Mateo and San Francisco counties. It does not include the mountainous or inland areas far removed from navigable waters. The geographic scope of potential impacts included in this consultation (action area) comprises the estuarine waters of the San Francisco Bay region, portions of the Sacramento-San Joaquin Delta (Delta) west of Sherman Island and the western portion of the Port of Sacramento and Port of Stockton deep water ship channels. It also includes the wetlands and shallow intertidal areas that form a margin around the Estuary and the tidal portions of its tributaries. -
Toxic Contaminants in the San Francisco Bay-Delta and Their Possible Biological Effects
TOXIC CONTAMINANTS IN THE SAN FRANCISCO BAY-DELTA AND THEIR POSSIBLE BIOLOGICAL EFFECTS DAVID J.H. PHILLIPS AQUATIC HABITAT INSTITUTE 180 Richmond Field Station 1301 South 46th Street Richmond, CA 94804 (415) 231-9539 August 26, 1987 CONTENTS Acknowledgments ................ (i) I . INTRODUCTION ................. 1 I1 . TRACE ELEMENTS IN THE BAY-DELTA . 5 A . Silver .................. 7 B . Copper .................. 40 C . Selenium ................. 68 D . Mercury .................111 E . Cadmium .................133 F . Lead ...................148 G . Zinc ................... 163 H . Chromium .................171 I. Nickel ..................183 J . Tin ...................194 K . Other Trace Elements ...........200 111 . ORGANOCHLORINES IN THE BAY-DELTA .......202 A . Polychlorinated Biphenyls ........205 B . DDT and Metabolites ...........232 C . Other Organochlorines ..........257 IV . HYDROCARBONS IN THE BAY-DELTA ........ 274 A . Introduction ..............274 B . Hydrocarbons in the San Francisco Estuary . 281 C . Summary .................304 V . BIOLOGICAL EFFECTS OF BAY-DELTA CONTAMINANTS . 306 A . The Benthos of the Bay-Delta ...... 307 B . Fisheries of the Bay-Delta ........ 319 C . Bird Populations ............ 351 D . Mammalian Populations. Including Man . 354 E . Bioassay Data ............. 359 VI . CONCLUSIONS ................. 377 Literature Cited .............. 382 ACKNOWLEDGMENTS Thanks are due to a large number of people for their contributions to this document. Staff at the Aquatic Habitat Institute have provided their support, encouragement and talent. These include Andy Gunther, Jay Davis, Susan Prather, Don Baumgartner and Doug Segar. Word processing services were provided by Ginny Goodwind, Emilia Martins, Renee Ragucci, Audi Stunkard, Lori Duncan, and Susan Prather. Tat Cheung and Johnson Tang of the County of Alameda Public Works Agency contributed their time and talent to the preparation of figures. Melissa Blanton copy-edited the text, surviving the requirements of the author in respect of Anglicisation of local terminologies. -
676Cover Copy
Conceptual Foundations for Modeling Bioaccumulation in San Francisco Bay RMP Technical Report by Aroon R. Melwani Ben K. Greenfield Donald Yee Jay A.Davis CONTRIBUTION NO. 676 SAN FRANCISCO ESTUARY INSTITUTE 4911 Central Avenue, Richmond, CA 94804 AUGUST p: 510-746-7334 (SFEI), f: 510-746-7300, 2012 www.sfei.org This report should be cited as: Melwani, A.R., Greenfield, B.K., Yee, D. and Davis, J.A. (2012). Conceptual Foundations for Modeling Bioaccumulation in San Francisco Bay. RMP Technical Report. Contribution No. 676. San Francisco Estuary Institute, Richmond, California. Conceptual Foundations for Modeling Bioaccumulation in San Francisco Bay Regional Monitoring Program Technical Report A.R. Melwani, B.K. Greenfield, D. Yee, and J.A. Davis San Francisco Estuary Institute SFEI Contribution # 676 Suggested Citation: Melwani, A.R., B.K. Greenfield, D. Yee, and J.A. Davis. 2012. Conceptual Foundations for Modeling Bioaccumulation in San Francisco Bay. SFEI Contribution # 676. San Francisco Estuary Institute, Richmond, CA. Final Report Table of Contents EXECUTIVE SUMMARY ______________________________________________ 4 1. Introduction________________________________________________________ 7 2. Target Chemicals: Bioaccumulation Processes and Biota Concentrations________ 8 Methylmercury _______________________________________________________ 9 Selenium ___________________________________________________________ 12 Polychlorinated Biphenyls (PCBs) _______________________________________ 13 Polybrominated Diphenyl Ethers (PBDEs) ________________________________ -
Urban Creeks Monitoring Report: Water Year 2020 (October 2019 – September 2020)
Urban Creeks Monitoring Report: Water Year 2020 (October 2019 – September 2020) Submitted to the San Francisco Bay and Central Valley Regional Water Quality Control Boards in Compliance with NPDES Permit Provision C.8.h.iii NPDES Permit Nos. CAS612008 and CAS083313 March 31, 2021 A Program of Contra Costa County, its Incorporated Cities and Towns, and the Contra Costa Flood Control & Water Conservation District This page intentionally blank Contra Costa Clean Water Program Urban Creeks Monitoring Report: Water Year 2020 (October 2019 – September 2020) March 31, 2021 Prepared for Contra Costa Clean Water Program 255 Glacier Drive Martinez, California 94553 Contra Costa Clean Water Program Participants • Cities of Antioch, Brentwood, Clayton, Concord, Danville (Town), El Cerrito, Hercules, Lafayette, Martinez, Moraga (Town), Oakley, Orinda, Pinole, Pittsburg, Pleasant Hill, Richmond, San Pablo, San Ramon, and Walnut Creek • Unincorporated Contra Costa County • Contra Costa County Flood Control & Water Conservation District Prepared by ADH Environmental 3065 Porter Street, Suite 101 Soquel, California 95073 In association with Wood Environment & Infrastructure Solutions, Inc. 180 Grand Avenue, Suite 1100 Oakland, California 94612 and Armand Ruby Consulting 2441 Rifle Range Drive Royal Oaks, California 95076 This page intentionally blank Urban Creeks Monitoring Report Water Year 2020 Table of Contents List of Acronyms and Abbreviations ............................................................................................................. -
Habitat Stressor Narrative Descriptions
SAN FRANCISCO BAY SUBTIDAL HABITAT GOALS REPORT Appendix 2-1: Habitat Stressor Narrative Descriptions ANDREW N. COHEN, SAN FRANCISCO ESTUARY INSTITUTE Contents 1. Sources and Impacts of Chemical Contaminants in San Francisco Bay 1 2. Sources and Impacts of Sediment Inputs into the Water column of San Francisco Bay 21 3. Impacts of the Removal or Disturbance of Sediments, Shells or Bedrock in San Francisco Bay 48 4. Impacts of Artificial Structures Placed in San Francisco Bay 63 5. Sources, Mechanisms and Impacts of Changes in Nutrient Inputs to San Francisco Bay 71 Sources and Impacts of Chemical Contaminants in San Francisco Bay Andrew N. Cohen, San Francisco Estuary Institute This paper discusses some of the major chemical contaminants in San Francisco Bay, including aspects of their sources, loading and pathways, and their impacts on organisms and human health. Inputs of nutrients into the Bay, considered a pollutant in some contexts, are addressed in the accompanying paper on "Sources, Mechanisms and Impacts of Changes in Nutrient Inputs to San Francisco Bay" (Cohen 2008). Exotic species, which are classified as a biological pollutant under the Clean Water Act and have been confirmed as such by recent federal court decisions, are addressed under the stressor "Release Exotic Organisms." A wide variety of contaminants have been the subject of regulation, monitoring or research in the Bay. With limited resources, this paper has relied substantially on recent review articles, which were available or more complete for some contaminants than for others. Accordingly, there is less text on some currently important contaminants than on certain contaminants of lesser or declining regulatory significance. -
Estuarine Data Index: a Guide to Bay-Delta Research and Monitoring
Estuarine Data Index: A Guide to Bay-Delta Research and Monitoring Programs Volume I Table of Contents Introduction ............................................. i Contaminant Loading ABAG Urban Runoff Studies ............................. 1 National Coastal Pollutant Discharge Inventory ................. 7 Santa Clara Valley Nonpoint Source Study ................... 12 NPDES Discharge Monitoring Database ..................... 20 Pesticide Use Reporting System .......................... 30 Sacramento Urban Runoff Monitoring Study .................. 41 US Coast Guard Spills Data ............................ 45 Western San Joaquin Valley Hydrogeologic Studies ............. 47 Hydrodynamics and Delta Inflow DAYFLOW ........................................ 52 Hydrodynamic Monitoring and Modeling ..................... 58 Water Resources Data ................................ 64 Sediments and Dredging Dredge Disposal Study ................................ 86 Dredging and Permitting .Sacramento District .................102 Dredging and Permitting . San Francisco District ...............107 Sediment Quality Survey ............................... 121 UDtake and Effects of Toxicants California State Mussel Watch Program .....................142 Uptake and Effects of Toxicants. cont'd . Chevron Deep Water Outfall Project ....................... 152 Contaminants of Concern: San Francisco Bay and San Pablo Bay National Wildlife Refuges ................. 163 National Status and Trends Program ....................... 168 Organic Contaminants in San Francisco -
727 Report Cover & IFC Davis
NUMBER 727 SEP 2014 PCBs in San Francisco Bay: Assessment of the Current State of Knowledge and Priority Information Gaps Prepared by: Jay Davis Lester McKee Thomas Jabusch Don Yee John Ross SAN FRANCISCO ESTUARY INSTITUTE 4911 Central Avenue, Richmond, CA 94804 • p: 510-746-7334 (SFEI) • f: 510-746-7300 • www.sfei.org This report should be cited as: Davis, J.A., L.J. McKee, T. Jabusch, D. Yee, and J.R.M. Ross. 2014. PCBs in San Francisco Bay: Assessment of the Current State of Knowledge and Priority Information Gaps. RMP Contribution No. 727. San Francisco Estuary Institute, Richmond, California. Final RMP Technical Report PCBs in San Francisco Bay: Assessment of the Current State of Knowledge and Priority Information Gaps J.A. Davis, L.J. McKee, T. Jabusch, D. Yee, J.R.M. Ross San Francisco Estuary Institute September 30, 2014 Executive Summary 1 Executive Summary In 2009 the RMP PCB Strategy Team articulated management questions to guide a long-term program of studies to support reduction of PCB impairment in the Bay. The objective of this technical report is to answer, to the extent possible, those PCB Strategy management questions based on the information that has accumulated to date. 1. What potential for impacts on humans and aquatic life exists due to PCBs? The potential for PCB impacts on humans through consumption of Bay fish is significant, especially for the TMDL indicator species (shiner surfperch and white croaker). High PCB concentrations at two locations (Oakland Harbor and San Francisco Waterfront) drove the Bay-wide average for shiner surfperch above the no consumption threshold established by the Office of Environmental Health Hazard Assessment. -
Aquatic Pesticide Application Plan for the San Francisco Estuary Invasive Spartina Project
Aquatic Pesticide Application Plan for the San Francisco Estuary Invasive Spartina Project This plan addresses herbicide application activities undertaken by the coalition of ISP partner agencies in the effort to eradicate non-native, invasive Spartina from the San Francisco Estuary. Annual update prepared by Drew Kerr 2612-A 8th Street Berkeley, CA 94710 [email protected] Under contract to Olofson Environmental, Inc. Berkeley, California for the State Coastal Conservancy 1330 Broadway, 13th floor Oakland, Ca 94612-2530 July 2012 Current funding for the San Francisco Estuary Invasive Spartina Project comes from the California State Coastal Conservancy and grants from the California Wildlife Conservation Board. Table of Contents Table of Contents ................................................................................................................................... i List of Figures ....................................................................................................................................... ii List of Tables ......................................................................................................................................... ii Appendices ............................................................................................................................................ ii 1. BACKGROUND ........................................................................................................ 1 2. STATEMENT OF PURPOSE AND NEED ............................................................... -
9. Suisun Bay Off Bull's Head Point Near Martinez Samples Are
6. Suisun Bay off Bull’s Head Point near 38-02-40 122-07-00 Martinez Samples are collected near the Southern Pacific Railroad bridge at Benicia. 7. Grizzly Bay at Dolphin near Suisun 38-07-02 122-02-19 Slough Samples are collected from a shallow embayment 1.4 miles east of the mouth of Suisun Slough. 8. Suisun Bay off Middle Point near 38-03-36 121 -59-20 Nichols Samples are collected in Suisun Bay within the west reach of the Middle Ground Channel. 9. Honker Bay near Wheeler point 38-04-26 121-56-1 2 The sampling site is located in a shallow embayment 1.9 miles northeasterly from Point Palo Alto. 10. Sacramento River at Chipps Island 38-02-47 12 1-55-02 Samples are collected west of the confluence of the Sacramento and San Joaquin Rivers between Chipps and Mallard Islands. 11. Sherman Lake near Antioch 38-02-34 12 1-47-34 Samples are collected 2 miles north of Antioch near the center of a submerged tract between the Sacramento and San Joaquin Rivers. 12. San Joaquin River at Antioch. Ship 38-01-1 5 121-48-28 Channel Samples are collected 0.3 miles north of Antioch between the entrance markers of the Antioch Reach Channel in the San Joaquin River. 13. Big Break near Oakley 38-01-05 121-42-38 The sampling site is located 1.3 miles north of Oakley in a submerged tract. 14. San Joaquin River at Jersey Point 38-03-09 121 -41 -1 7 This sampling site is located on the San Joaquin River 6.5 miles northeast of Antioch in the shipping channel. -
Mon Toring of Toxic Contaminants in the San Francisco Bay-Delta
Aquatic Habitat Institute MON TORING OF TOXIC CONTAMINANTS IN THE SAN FRANCISCO BAY-DELTA: A CRITICAL REVIEW, EMPHASIZING SPATIAL AND TEMPORAL TREND MONITORING DAVID J.H. PHILLIPS Aquatic Habitat Institute, 180 Richmond Field Station, 1301 South 46th. Street, Richmond, CA 94804, USA. December 980 Son Francisco Bay - Delta CONTENTS Acknowledgements (i1 Preface (ii) I. Introduction 1 A. Contaminants in the Estuary: Historical and Existing Concerns 1 9. Management Issues Related to Contaminants 5 C. Goals and Contents of This Report 13 II. Available Methods for Monitoring Toxic Contaminants in Estuaries 16 A. Alternative Approaches: Water, Sediment, Biota 16 9. Bio-monitoring Techniques: Early Development 23 C. Improvements and Important Concepts 24 D. Review of Bio-monitoring Organisms 28 E. Conclusions on Bio-monitoring Techniques 46 111. Toxic Contaminants of Greatest Concern in the Estuary 47 IV. Regional Monitoring of Toxic Contaminants in the Estuary 53 A. Introduction 53 9. Regional Monitoring of Toxic Contaminants in Ambient Waters 56 C. Regional Monitoring of Toxic Contaminants in Sediments 75 D. Regional Monitoring of Toxic Contaminants in Biota 84 V. Local Monitoring of Toxic Contaminants in the Estuary 13 A. Introduction 13 8. Monitoring of Contaminant Concentrations in Effluents 16 C. Bioassays of Effluents 24 D. Studies Close to Effluent Outfalls 28 E. The Case for Local Bio-accumulation Studies 39 VI. The Monitoring of Toxicants in Target Species and Food Chains 44 VII. The Proposed Monitoring Program 48 A. General Description of the Proposed Program 148 6. Selection of Study Sites 158 C. Species to be Employed in Bio-monitoring Studies 168 D. -
Aquatic Pesticide Application Plan for the San Francisco Estuary Invasive Spartina Project
Aquatic Pesticide Application Plan for the San Francisco Estuary Invasive Spartina Project This plan addresses herbicide application activities undertaken by ISP Partner agencies in the effort to eradicate non-native, invasive Spartina from the San Francisco Estuary. Annual update prepared by Drew Kerr 2612-A 8th Street Berkeley, CA 94710 [email protected] for the State Coastal Conservancy 1330 Broadway, 13th floor Oakland, Ca 94612-2530 August 2010 Current funding for the San Francisco Estuary Invasive Spartina Project comes from the California State Coastal Conservancy and grants from the U.S. Environmental Protec- tion Agency, the National Oceanic and Atmospheric Administration and the U.S. Miner- als Management Service. Previous major funders include the CALFED Bay-Delta Pro- gram, the California Wildlife Conservation Board, the U.S. Fish and Wildlife Service and the National Fish and Wildlife Foundation. Table of Contents 1. BACKGROUND ........................................................................................................ 1 2. STATEMENT OF PURPOSE AND NEED................................................................ 1 3. DESCRIPTION OF THE WATER BODY SYSTEM................................................. 2 Ecology................................................................................................................................... 2 Natural Processes Affecting Water Quality............................................................................ 3 Water Quality.........................................................................................................................