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Report
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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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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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Foley, M. M.; Davis, J. A.; Buzby, N. 2024. Selenium Concentrations in Water and Clams in North San Francisco Bay, 2019-2020. SFEI Contribution No. 1116. San Francisco Estuary Institute: Richmond, CA.

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) started implementing a new design for North Bay selenium (Se) sampling in 2019 after a long-term USGS program was terminated in 2017. To determine if the RMP sampling and analysis methods are producing similar results to the USGS study, we compared Se concentrations and stable isotope values in clams at two stations in Suisun Bay, California, that were sampled by the USGS long-term monitoring program from 1995-2010 and the RMP in 2019-2020. We also compared Se concentrations in water (dissolved and particulate) from the RMP Status and Trends sampling in Suisun Bay (1993-2019) to the samples collected as part of this study. 

Spatial patterns in clam Se concentrations between the USGS and RMP studies were similar, with lower concentrations at Station 4.1 (Suisun Bay) than at Station 8.1 (Carquinez Strait). Se concentrations at both stations were consistently lower for the RMP samples than those reported in the long-term USGS dataset. Stable isotope values for δ13C and δ15N were similar for the USGS and RMP samples with δ13C and δ15N more enriched at Station 8.1 than 4.1. However, there was not close alignment of the RMP samples to the USGS long-term average, particularly at Station 8.1. Average dissolved Se concentrations in water were consistently lower than the long-term average at Station 4.1 and similar to or above the long-term RMP Status and Trends (S&T) average at Station 8.1. Particulate Se concentrations at Stations 4.1 and 8.1 were nearly one-third of the long-term S&T average in Suisun Bay, likely due to a change in methods for calculating particulate Se. 

Additional information is needed to evaluate whether the lower Se concentrations measured in clams as part of the RMP study could be suggestive of declining Se concentrations in North Bay clams between 2010 and 2019 or an artifact of the new analytical lab. Additional data from samples collected by the USGS from 2011-2017 should be examined to fill the gap between the datasets. Continued RMP monitoring will also be valuable in evaluating long-term trends.

 

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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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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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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.
Davis, J. A. 2002. A PCB Budget for San Francisco Bay. SFEI Contribution No. 376. San Francisco Estuary Institute: Oakland, CA.
Oram, J. J.; Greenfield, B. K.; Davis, J. A.; David, N.; Leatherbarrow, J. E. 2006. Organochlorine Pesticide Fate in San Francisco Bay. SFEI Contribution No. 433. San Francisco Estuary Institute: Oakland, CA. p 48.
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Jarman, W. M.; Davis, J. A. 1997. Observations on trace organic concentrations in RMP water samples. SFEI Contribution No. 210. San Francisco Estuary Institute. pp 67-77.
Grieb, T.; Roy, S.; Rath, J.; Stewart, R.; Sun, J.; Davis, J. A. 2018. North Bay Selenium Monitoring Design. SFEI Contribution No. 921. San Francisco Estuary Institute : Richmond, CA.
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Robinson, A.; Slotton, D. G.; Lowe, S.; Davis, J. A. 2014. North Bay Mercury Biosentinel Project (December 2014 Report). SFEI Contribution No. 738. San Francisco Estuary Institute: Richmond, CA.
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Kleckner, A.; Davis, J. 2024. Multi Year Plan 2024. SFEI Contribution No. 1167. San Francisco Estuary Institute: Richmond, CA.

The purpose of this document is to guide efforts and summarize plans developed within the RMP. The intended audience includes representatives of the many organizations who directly participate in the Program. This document will also be useful for individuals who are not directly involved with the RMP but are interested in an overview of the Program and where it is heading.


The organization of this Multi-Year Plan parallels the RMP planning process (Figure 2). Section 1 presents the long-term management plans of the agencies responsible for managing water quality in the Bay and the overarching management questions that guide the Program. The agencies’ long-term management plans provide the foundation for RMP planning (Figure 2). In order to turn the plans into effective actions, the RMP distills prioritized lists of management questions that need to be answered (Page 8). The prioritized management questions then serve as a roadmap for scientists on the Technical Review Committee, workgroups, and strategy teams to plan and implement scientific studies to address the most urgent information needs. This information sharpens the focus on management actions that will most effectively and efficiently

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Foley, M.; Davis, J.; Yee, D. 2023. Multi-Year Plan 2023. SFEI Contribution No. 1096. San Francisco Estuary Institute: Richmond, California.

The purpose of this document is to guide efforts and summarize plans developed within the RMP. The intended audience includes representatives of the many organizations who directly participate in the Program. This document will also be useful for individuals who are not directly involved with the RMP but are interested in an overview of the Program and where it is heading.  

The organization of this Multi-Year Plan parallels the RMP planning process (Figure 2). Section 1 presents the long-term management plans of the agencies responsible for managing water quality in the Bay and the overarching management questions that guide the Program. The agencies’ long-term management plans provide the foundation for RMP planning (Figure 2). In order to turn the plans into effective actions, the RMP distills prioritized lists of management questions that need to be answered (Page 8). The prioritized management questions then serve as a roadmap for scientists on the Technical Review Committee, workgroups, and strategy teams to plan and implement scientific studies to address the most urgent information needs. This information sharpens the focus on management actions that will most effectively and efficiently improve water quality in the Bay. 

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Greenfield, B. K.; Ichikawa, G.; Stephenson, M.; Davis, J. A. 2002. Mercury in Sport Fish from the Delta Region (Task 2A). SFEI Contribution No. 252. San Francisco Estuary Institute / CALFED Final Project Report.: Oakland, CA. p 88 pp.
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Davis, J. A. 1988. Inventory of Priority Datasets Relating to the San Francisco Estuary. SFEI Contribution No. 141. San Francisco Estuary Institute: Richmond, CA. p 51.
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Gunther, A. J.; Davis, J. A. 1998. An evaluation of bioaccumulation monitoring with transplanted bivalves in the RMP. SFEI Contribution No. 322. San Francisco Estuary Institute: Richmond, CA. pp 187-200.
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Clark, S.; Bailey, H. C.; Davis, J. A. 1995. The Effects of Toxic Contaminants in Waters of the San Francisco Bay and Delta. SFEI Contribution No. 184. Prepared for Bay/Delta Oversight Council: Sacramento, CA. p 125 pp.
Davis, J. A. 1986. Ecological guidelines for the use of natural wetlands for municipal wastewater management in North Carolina. SFEI Contribution No. 134. Division of Environmental Management, North Carolina Department of Natural Resources and Community Development: Raleigh, NC.
Oram, J. J.; Leatherbarrow, J. E.; Davis, J. A. 2005. DRAFT REPORT: A Model of Long-Term PCB Fate and Transport in San Francisco Bay, CA. SFEI Contribution No. 388. San Francisco Estuary Institute: Oakland, CA.
Connor, M.; Yee, D.; Davis, J. A.; Werme, C. 2004. Dioxins in San Francisco Bay: Conceptual Model/Impairment Assessment. SFEI Contribution No. 309. San Francisco Estuary Institute: Oakland. p 60.
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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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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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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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