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Greenfield, B. K.; Davis, J. A.; Collins, J. N.; Grenier, J. Letitia. 2002. The tidal marsh food web. SFEI Contribution No. 472. University of California: Berkeley, CA. p 12 pp.
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Davis, J. A.; Gunther, A. J.; Abu-Saba, K. E. 2001. Technical Report of the Sources, Pathways, and Loadings Workgroup. SFEI Contribution No. 266. San Francisco Estuary Institute: Richmond, CA.
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Davis, J. A.; Yoon, J. 1999. Technical Report of the Chlorinated Hydrocarbon Workgroup. San Francisco Estuary Institute: Richmond, CA.
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Lin, D.; Davis, J. 2018. Support for Sediment Bioaccumulation Evaluation: Toxicity Reference Values for the San Francisco Bay. SFEI Contribution No. 916. San Francisco Estuary Institute : Richmond, CA.
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Jones, C.; Davis, J.; Yee, D. 2022. Strategy for In-Bay Fate Modeling to Support Contaminant and Sediment Management in San Francisco Bay. SFEI Contribution No. 1090. San Francisco Estuary Institute: Richmond, California.

This report presents a strategy and multi-year workplan for modeling polychlorinated biphenyls (PCBs), contaminants of emerging concern (CECs), and sediment in San Francisco Bay (the Bay). Robust in-Bay fate modeling is needed to address priority management questions that have been identified for these constituents.

The strategy for in-Bay modeling presented in this report is a major element of a broader, integrated strategy that is being developed across RMP Workgroups for modeling contaminants flowing from the Bay watersheds and other pathways into the Bay. The broader project is expected to yield an integrated strategy in 2022, followed by implementation of a pilot effort in 2023. Coordination of the in-Bay modeling effort with the broader integrated strategy and other modeling work (e.g., nutrient modeling under the Nutrient Management Strategy) will be critical to optimizing use of the funds allocated to modeling.

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Connor, M. S.; Davis, J. A. 2008. The State of San Francisco Bay: Water Quality. National Water Quality Monitoring Conference.
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Davis, J. A.; Connor, M. S.; Flegal, A. R.; Conaway, C. H. 2007. Sources, transport, fate and toxicity of pollutants in the San Francisco Bay estuary. Environmental Research : A Multidisciplinary Journal of Environmental Sciences, Ecology and Public Health 105, 1-4.
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Oram, J. J.; McKee, L. J. .; Davis, J. A.; Sedlak, M.; Yee, D. 2008. Sources, Pathways and Loadings Workgroup: Five-Year Workplan (2008-12). SFEI Contribution No. 567. San Francisco Estuary Institute: Oakland.
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Greenfield, B. K.; Davis, J. A. 2004. A Simple Mass Balance Model for PAH Fate in the San Francisco Estuary. SFEI Contribution No. 115. San Francisco Estuary Institute: Oakland, CA.
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Sun, J.; Davis, J. A.; Stewart, R.; Palace, V. 2019. Selenium in White Sturgeon from North San Francisco Bay: The 2015-2017 Sturgeon Derby Study. SFEI Contribution No. 897. San Francisco Estuary Institute: Richmond, CA.

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) tissues collected during the 2015-2017 Sturgeon Derby events in North San Francisco Bay. The goal of this study was to investigate the distribution of selenium among sturgeon tissues to inform the toxicological and regulatory interpretation of selenium measured in non-lethally collected tissues, including muscle plugs and fin rays. This technical report provides documentation of the study and presents its major findings.

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Sun, J.; Davis, J.; Stewart, R. 2018. Selenium in Muscle Plugs of White Sturgeon from North San Francisco Bay, 2015-2017. SFEI Contribution No. 929. San Francisco Estuary Institute : Richmond, CA.
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Davis, J.; Yee, D.; Fairey, R.; Sigala, M. 2017. San Leandro Bay PCB Study Data Report. SFEI Contribution No. 855. San Francisco Estuary Institute: Richmond, CA.
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McKee, L.; Peterson, D.; Braud, A.; Foley, M.; Dusterhoff, S.; Lowe, J.; King, A.; Davis, J. 2023. San Francisco Bay Sediment Modeling and Monitoring Workplan. SFEI Contribution No. 1100. San Francisco Estuary Institute: Richmond, CA.

This document was prepared with guidance gained through two RMP Sediment Workgroup workshops held in late 2022 and early 2023. Given the variety of participants involved, this Workplan encompasses interests beyond San Francisco Bay RMP funders. We thank the attendees for their contributions. 

In 2020, the Sediment Workgroup (SedWG) of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) completed a Sediment Monitoring and Modeling Strategy (SMMS) which laid out a conceptual level series of data and information gaps and generally recommended the use of both empirical data collection and modeling tools to answer initial high priority management questions (McKee et al., 2020). At the time, the SMMS promoted the use of surrogates such as time-continuous turbidity measurements for cross-section flux modeling within the Bay without an understanding of existing Bay hydrodynamic models, their strengths, weaknesses, and potential uses for understanding coupled Bay-mudflat-marsh processes. Since then, the Wetland Regional Monitoring Program (WRMP, www.wrmp.org) has generally promoted the use of coupling monitoring and modeling techniques to inform wetlands sediment management decisions. In addition, he completion of the Sediment for Survival report (a RMPEPA funded collaboration) and the further development of sediment conceptual models has also advanced the need for a coupled dynamic modeling and monitoring program that has the capacity to explore more complex management questions (Dusterhoff et al., 2021; SFEI, 2023). Such a program will take time to develop, but will be more cost-efficient and adaptable and allow for more timely answers to pressing questions. 

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Hunt, J.; Trowbridge, P.; Yee, D.; Franz, A.; Davis, J. 2016. Sampling and Analysis Plan for 2016 RMP Status and Trends Bird Egg Monitoring. SFEI Contribution No. 827. San Francisco Estuary Institute: Richmond, CA. p 31 pp.
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Davis, J.; Foley, M.; Askevold, R.; Chelsky, A.; Dusterhoff, S.; Gilbreath, A.; Lin, D.; Yee, D.; Senn, D.; Sutton, R. 2021. RMP Update 2021. SFEI Contribution No. 1057.

The overarching goal of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is to answer the highest priority scientific questions faced by managers of Bay water quality. The RMP is an innovative collaboration between the San Francisco Bay Regional Water Quality Control Board, the regulated discharger community, the San Francisco Estuary Institute, and many other scientists and interested parties. The purpose of this document is to provide a concise overview of recent RMP activities and findings, and a look ahead to significant products anticipated in the next two years. The report includes a description of the management context that guides the Program; a brief summary of some of the most noteworthy findings of this multifaceted Program; and a summary of progress to date and future plans for addressing priority water quality topics.

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Davis, J.; Foley, M.; Askevold, R.; Buzby, N.; Chelsky, A.; Dusterhoff, S.; Gilbreath, A.; Lin, D.; Miller, E.; Senn, D.; et al. 2020. RMP Update 2020. SFEI Contribution No. 1008.

The overarching goal of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is to answer the highest priority scientific questions faced by managers of Bay water quality. The RMP is an innovative collaboration between the San Francisco Bay Regional Water Quality Control Board, the regulated discharger community, the San Francisco Estuary Institute, and many other scientists and interested parties. The purpose of this document is to provide a concise overview of recent RMP activities and findings, and a look ahead to significant products anticipated in the next two years. The report includes a description of the management context that guides the Program; a brief summary of some of the most noteworthy findings of this multifaceted Program; and a summary of progress to date and future plans for addressing priority water quality topics.

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Trowbridge, P. R.; Davis, J. A.; Mumley, T.; Taberski, K.; Feger, N.; Valiela, L.; Ervin, J.; Arsem, N.; Olivieri, A.; Carroll, P.; et al. 2016. The Regional Monitoring Program for Water Quality in San Francisco Bay, California, USA: Science in support of managing water quality. Regional Studies in Marine Science 4.

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is a novel partnership between regulatory agencies and the regulated community to provide the scientific foundation to manage water quality in the largest Pacific estuary in the Americas. The RMP monitors water quality, sediment quality and bioaccumulation of priority pollutants in fish, bivalves and birds. To improve monitoring measurements or the interpretation of data, the RMP also regularly funds special studies. The success of the RMP stems from collaborative governance, clear objectives, and long-term institutional and monetary commitments. Over the past 22 years, high quality data and special studies from the RMP have guided dozens of important decisions about Bay water quality management. Moreover, the governing structure and the collaborative nature of the RMP have created an environment that allowed it to stay relevant as new issues emerged. With diverse participation, a foundation in scientific principles and a continual commitment to adaptation, the RMP is a model water quality monitoring program. This paper describes the characteristics of the RMP that have allowed it to grow and adapt over two decades and some of the ways in which it has influenced water quality management decisions for this important ecosystem.

Davis, J. A. 2005. Regional Monitoring Program for Trace Substances in the San Francisco Estuary 2005 Program Plan. SFEI Contribution No. 389. San Francisco Estuary Institute: Oakland. p 16.
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Gunther, A. J.; O'Connor, J. M.; Davis, J. A. 1992. Priority pollutant loads from effluent discharges to the San Francisco Estuary. Water Environment Research 64, 134-140 . SFEI Contribution No. 171.
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Oram, J. J.; McKee, L. J. .; Davis, J. A.; Hetzel, F. 2007. Polychlorinated biphenyls (PCBs) in San Francisco Bay. Environmental Research 105, 67-86 . SFEI Contribution No. 526.
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Sutton, R.; Sedlak, M.; Davis, J. A. 2014. Polybrominated Diphenyl Ethers (PBDEs) in San Francisco Bay: A Summary of Occurrence and Trends. SFEI Contribution No. 713. San Francisco Estuary Institute: Richmond, CA. p 62.
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Leatherbarrow, J. E.; Yee, D.; Davis, J. A. 2001. PCBs in effluent. SFEI Contribution No. 237.
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Davis, J. A. 2002. A PCB Budget for San Francisco Bay. SFEI Contribution No. 376. San Francisco Estuary Institute: Oakland, CA.
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Greenfield, B. K.; Davis, J. A. 2004. A PAH Fate Model for San Francisco Bay. Chemosphere . SFEI Contribution No. 114.
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