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Davis, J. A.; Lowe, S.; Anderson, B.; Hunt, J.; Thompson, B. 2004. Conceptual Framework and Rationale for the Exposure and Effects Pilot Study. SFEI Contribution No. 317. San Francisco Estuary Institute: Oakland.
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Collins, J. N.; Brewster, E.; Grossinger, R. M. 1999. Conceptual models of freshwater influences on tidal marsh form and function, with an historical perspective. SFEI Contribution No. 327. Department of Environmental Services: City of San Jose, CA. p 237 pp.
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Yee, D.; Gilbreath, A. N.; McKee, L. J. .; Davis, J. A. 2019. Conceptual Model to Support PCB Management and Monitoring in the San Leandro Bay Priority Margin Unit - Final Report. SFEI Contribution No. 928. San Francisco Estuary Institute: Richmond, CA.

The goal of RMP PCB special studies over the next few years is to inform the review and possible revision of the PCB TMDL and the reissuance of the Municipal Regional Permit for Stormwater, both of which are tentatively scheduled to occur in 2020. Conceptual model development for a set of four representative priority margin units will provide a foundation for establishing an effective and efficient monitoring plan to track responses to load reductions, and will also help guide planning of management actions. The Emeryville Crescent was the first PMU to be studied in 2015-2016. The San Leandro Bay PMU is second (2016-2018), Steinberger Slough in San Carlos is third (2018), and Richmond Harbor will be fourth (2018-2019).

This document is Phase Three of a report on the conceptual model for San Leandro Bay. A Phase One report (Yee et al. 2017) presented analyses of watershed loading, initial retention, and long-term fate, including results of sediment sampling in 2016. A Phase Two data report (Davis et al. 2017) documented the methods, quality assurance, and all of the results of the 2016 field study. This Phase Three report is the final report that incorporates all of the results of the 2016 field study, and includes additional discussion of the potential influence of contaminated sites in the
watershed, the results of passive sampling by Stanford researchers and a comparative analysis of long-term fate in San Leandro Bay and the Emeryville Crescent, a section on bioaccumulation, and a concluding section with answers to the management questions that were the impetus for the work.

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McKnight, K.; Braud, A.; Dusterhoff, S.; Grenier, L.; Shaw, S.; Lowe, J.; Foley, M.; McKee, L. 2023. Conceptual Understanding of Fine Sediment Transport in San Francisco Bay. SFEI Contribution No. 1114. San Francisco Estuary Institute: Richmond, CA.

Sediment is a lifeblood of San Francisco Bay (Bay). It serves three key functions: (1) create and maintain tidal marshes and mudflats, (2) transport nutrients and contaminants, and (3) reduce impacts from excessive human-derived nutrients in the Bay. Because of these important roles, we need a detailed understanding of sediment processes in the Bay.


This report offers a conceptual understanding of how fine-grained sediment (i.e. silt and finer, henceforth called fine sediment) moves around at different scales within the Bay, now and into the future, to synthesize current knowledge and identify critical knowledge gaps. This information can be used to support Bay sediment management efforts and help prioritize funding for research and monitoring. In particular, this conceptual understanding is designed to inform future San Francisco Bay Regional Monitoring Program (RMP) work under the guidance of the Sediment Workgroup of the RMP for Water Quality in San Francisco Bay, which brings together experts who have worked on many different components of the landscape, including watersheds and tributaries, marshes and mudflats, beaches, and the open Bay. This report describes sediment at two scales: a conceptual understanding of open-Bay sediment processes at the Bay and subembayment scale (Chapter 2); and a conceptual understanding of sediment processes at the baylands scale (Chapter 3). Chapter 4 summarizes the key knowledge gaps and provides recommendations for future studies.

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Greenfield, B. K.; Davis, J. A.; Fairey, R.; Ichikawa, G.; Roberts, C.; Crane, D. B.; Petreas, M. 2003. Contaminant Concentrations in Fish from San Francisco Bay, 2000. San Francisco Estuary Institute, Moss Landing Marine Laboratories, Water Pollution Control Laboratories, California Department of Fish and Game, Hazardous Materials Laboratory, Cal/EPA: Oakland, CA.
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McKee, L. J. .; Hoenicke, R.; Leatherbarrow, J. E. 2001. Contaminant contributions from the Guadalupe River and Coyote Creek watersheds to the lower South San Francisco Bay. Abstracts of the 5th Biannual State of the Estuary Conference – San Francisco Estuary: Achievements, trends and the future.
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Davis, J. A.; McKinney, M.; Mok, M.; Stoelting, M.; Wainwright, S. E.; May, M. D.; Petreas, M.; Roberts, C.; Taberski, K.; Tjeerdema, R. S.; et al. 1999. Contaminants Concentrations in Fish from San Francisco Bay, 1997. SFEI Contribution No. 35. San Francisco Estuary Institute, Richmond, CA, Moss Landing Marine Laboratories, Moss Landing, CA, Hazardous Materials Laboratory, Cal/EPA, Berkeley, CA, Institute of Marine Sciences, University of California, Santa Cruz, CA, San Francisco Bay Regional Wa: Richmond, CA.
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Sutton, R.; Sedlak, M. 2015. Contaminants of Emerging Concern in San Francisco Bay: A Strategy for Future Investigations. 2015 Update. Contaminants of Emerging Concern in San Francisco Bay: A Strategy for Future Investigations. SFEI Contribution No. 761. San Francisco Estuary Institute: Richmond, CA.

About this Update

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) has been investigating contaminants of emerging concern (CECs) since 2001. CECs can be broadly defined as synthetic or naturally occurring chemicals that are not regulated or commonly monitored in the environment but have the potential to enter the environment and cause adverse ecological or human health impacts.

The RMP Emerging Contaminants Workgroup (ECWG), established in 2006, includes representatives from RMP stakeholder groups, regional scientists, and an advisory panel of expert researchers that work together to address the workgroup’s guiding management question – Which CECs have the potential to adversely impact beneficial uses in San Francisco Bay? The overarching goal of the ECWG is to develop cost-effective strategies to identify and monitor CECs to minimize impacts to the Bay.

To this end, the RMP published a CEC Strategy document in 2013 (Sutton et al. 2013). The strategy is a living document that guides RMP special studies on CECs, assuring continued focus on the issues of highest priority to the health of the Bay. A key focus of the strategy is a tiered risk and management action framework that guides future monitoring proposals. The strategy also features a multi-year plan indicating potential future research priorities.

This 2015 CEC strategy update features revised designations of CECs in the tiered risk and management action framework based on monitoring and research conducted since 2013. Brief summaries of relevant RMP findings are provided. In addition, a proposed multi-year plan for future RMP Special Studies on CECs is outlined. A full revision of the CEC strategy is anticipated in 2016. 

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Miller, E.; Mendez, M.; Shimabuku, I.; Buzby, N.; Sutton, R. 2020. Contaminants of Emerging Concern in San Francisco Bay: A Strategy for Future Investigations 2020 Update. SFEI Contribution No. 1007. San Francisco Estuary Institute: Richmond, CA.

This 2020 CEC Strategy Update is a brief summary document that describes the addition of recently monitored CECs to the tiered risk-based framework. Reviews of findings relevant to San Francisco Bay are provided, as is a discussion of the role of environmental persistence in classifying CECs within the framework. The Strategy is a living document that guides RMP special studies on CECs, assuring continued focus on the issues of highest priority to protecting the health of the Bay. A key focus of the Strategy is a tiered risk-based framework that guides future monitoring proposals. The Strategy also features a multi-year plan indicating potential future research priorities.

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Collins, J. N.; May, M. 1998. Contamination of Tidal Wetlands. SFEI Contribution No. 228. Richmond CA.
Salomon, M.; San Francisco Estuary Institute; Costa, Cof Contra. 2011. Contra Costa County 1939 Aerial Photomosaic, GIS layer containing orthorectified historical aerial imagery of Contra Costa County from 1939.
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Lowe, S.; Pearce, S.; Kauhanen, P.; Collins, J.; Titus, D. 2021. Coyote Creek Watershed Reassessment 2020: 10-Year Reassessment of the Ecological Condition of Streams Applying the California Rapid Assessment Method, Santa Clara County, California. SFEI Contribution No. 1043. San Francisco Estuary Institute: Richmond. CA. p 131.

This report describes the amount and distribution of aquatic resources in the Coyote Creek watershed, Santa Clara County, California, and presents the first reassessment of stream ecosystem conditions using a watershed approach and the California Rapid Assessment Method (CRAM). Field work was conducted in 2020, ten years after the baseline watershed assessment completed in 2010.

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Lowe, S. 2020. Coyote Creek Watershed Reassessment 2020 Ambient Stream Condition Survey Design and Monitoring Plan: A Review of the Original 2010 Survey Design and Development of the 2020 Reassessment Strategy. Pearce, S., Ed.; Titus, D., Tran.. SFEI Contribution No. 1055. San Francisco Estuary Institute: Richmond. CA. p 18.

This technical report describes the ten-year ambient stream condition reassessment survey design and monitoring plan (or strategy) for the Coyote Creek watershed. Because the reassessment employed (and modified) the 2010 sample draw, essential background information about the original 2010 probability-based survey design, sample draw, and field assessment outcomes were provided.

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Collins, J. N. 2007. CRAM Evaluation of Wetland Conditions. SFEI Contribution No. 544. Elk Grove, California. p 15.
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Hoenicke, R. 1997. Creating data-quality objectives: A case study. Water Environment Laboratory Solutions 7-9 . SFEI Contribution No. 31.
Lowe, S.; Robinson, A.; Frontiera, P.; Cayce, K.; Collins, J. N. 2014. Creating Landscape Profiles of Aquatic Resource Abundance, Diversity and Condition. SFEI Contribution No. 725. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 21.
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Ridolfi, K.; Hoenicke, R.; Van Velsor, K. 2007. Critical Coastal Areas Program, Phase I Final Report. SFEI Contribution No. 541. San Francisco Estuary Institute.
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Yee, D.; Wong, A.; Hetzel, F. 2018. Current Knowledge and Data Needs for Dioxins in San Francisco Bay. SFEI Contribution No. 926. San Francisco Estuary Institute : Richmond, CA.
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Heberger, M.; Sutton, R.; Buzby, N.; Sun, J.; Lin, D.; Mendez, M.; Hladik, M.; Orlando, J.; Sanders, C.; Furlong, E. 2020. Current-Use Pesticides, Fragrance Ingredients, and Other Emerging Contaminants in San Francisco Bay Margin Sediment and Water. SFEI Contribution No. 934. San Francisco Estuary Institute: Richmond, CA.

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) has recently focused attention on better characterization of contaminants in nearshore “margin” areas of San Francisco Bay. The margins of the Lower South Bay are mudflats and shallow regions that receive direct discharges of stormwater and wastewater; as a result, they may have higher levels of urban contaminants than the open Bay. In the summer of 2017, the RMP collected samples of margin
sediment in the South and Lower South Bay for analysis of legacy contaminants. The study described here leveraged that sampling effort by adding monitoring of sediment and water for two additional sets of emerging contaminants: 1) current-use pesticides; and 2) fragrance ingredients including the polycyclic musk galaxolide, as well as a range of other commonly detected emerging contaminants linked to toxicity concerns such as endocrine disruption.

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Palenik, B.; Flegal, R. A. 1999. Cyanobacterial Populations in San Francisco Bay. SFEI Contribution No. 42. San Francisco Estuary Institute: Richmond, CA.
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Cohen, A. N. 1997. Damming the Bay. Switzer Fellowship Network 5, 1,4.
Cohen, A. N. 1996. Damming the Bay. Watershed 35, 6-8.
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Kucera, T.; Breauz, A.; Zielinski, W. 2002. Data Collection Protocol Montioring River Otter (Lutra [=Lontra] canadensis). SFEI Contribution No. 241. CA State University Stanislaus, U.S Forest Service, San Francisco Bay Regional Water Quality Control Board: Oakland, CAStanislaus, CA. p 11.
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Siegel, S.; Callaway, J. 2002. Data Collection Protocol Sedimentation- Erosion Tables (SET's). SFEI Contribution No. 244. University of San Francisco, Wetlands and Water Resources: San Francisco, CASan Rafael, CA.
Vasey, M.; Callaway, J.; Parker, T. V. 2002. Data Collection Protocol Tidal Wetland Vegetation. SFEI Contribution No. 279. San Francisco State: San Francisco, CA. p 13.
Johnston, D. 2002. Data Collection Protocol Yuma Bat (Myotis yumanensis). SFEI Contribution No. 259. H.T Harvey & Associates: San Jose, CA. p 7.
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Flegal, A. R.; Squire, S.; Scelfo, G. H.; Revenaugh, J. 2002. Decadal trends of silver and lead contamination in San Francisco Bay surface waters. Environmental Science and Techology 36, 2379-2386 . SFEI Contribution No. 276.
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