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Foley, M. 2019. 2019 Bay RMP Multi-Year Plan. SFEI Contribution No. 940. San Francisco Estuary Institute: Richmond, CA.
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Buzby, N.; Yee, D.; Salop, P.; Foley, M. 2020. 2019 RMP North Bay Selenium Monitoring Sampling and Analysis Plan. SFEI Contribution No. 969. San Francisco Estuary Institute: Richmond, CA.

The goal of monitoring for selenium in the North Bay tissue and water is to identify leading indicators of change to allow prompt management response to signs of increasing impairment. At the 2016 technical workshop, participants reached a consensus that monitoring sturgeon, clams, and water are all needed to answer management questions. Recommendations for long-term monitoring of these three matrices are detailed in the North Bay Monitoring Design document (Grieb et al. 2018). The purpose of this Sampling and Analysis Plan is to clearly document the sampling design, methods, and responsibilities; and to facilitate coordination among project partners.

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Buzby, N.; Yee, D.; Foley, M.; David, J.; Sigala, M.; Bonnema, A. 2020. 2019 Sport Fish Monitoring Sampling and Analysis Plan. SFEI Contribution No. 970. San Francisco Estuary Institute: Richmond, CA.

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) monitors concentrations of contaminants in fish tissue as indicators of bioaccumulation of contaminants in the Bay. In 2019, the RMP will conduct its eighth round of sport fish monitoring by collecting sport fish samples from various locations in the Bay as a part of routine Status and Trends Monitoring. Add-ons to the routine Status and Trends sport fish monitoring design will include archiving for microplastics and fipronil, as well as additional collections of shiner surfperch in Priority Margin Unit areas (PMUs).

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Foley, M. 2019. 2020 RMP Multi-Year Plan. SFEI Contribution No. 959. San Francisco Estuary Institute: Richmond, CA.
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Foley, M. 2021. 2021 RMP Multi-Year Plan. SFEI Contribution No. 1027. San Francisco Estuary Institute: Richmond, CA.
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Foley, M.; Sutton, R.; Yee, D.; Salop, P. 2021. 2021 RMP Water Cruise Plan. SFEI Contribution No. 1050. San Francisco Estuary Institute: Richmond, California.

This report details plans associated with the annual Regional Monitoring Program for Water Quality in the San Francisco Estuary (RMP) water cruise. The RMP water sampling program was redesigned in 2002 to adopt a randomized sampling design at thirty-one sites in place of the twenty-six base program stations sampled previously. In 2007, the number of sites was decreased to twenty-two stations, and it remains as such for 2021. The analytes for 2021 have been modified based on the Status and Trends (S&T) Review process that started in 2020. The analytes that are being removed from the program include selenium and methylmercury (dissolved and particulate), while bisphenols and organophosphate esters (OPEs) have been added to S&T monitoring. 

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Davis, J.; Foley, M.; Askevold, R. A.; Sutton, R.; Senn, D.; Plane, E. 2022. 2022 Pulse of the Bay. SFEI Contribution No. 1095. San Francisco Estuary Institute: Richmond, California.

The theme of the 2022 Pulse is "50 Years After the Clean Water Act." Nine different individuals or groups have contributed perspectives on progress to date and challenges ahead. This Pulse also includes summaries, from a historical perspective, on the major water quality parameters of concern in the Bay.   

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Foley, M. M. 2022. 2022 RMP Multi-Year Plan. SFEI Contribution No. 1058. San Francisco Estuary Institute: Richmond, California.
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Foley, M. 2022. 2023 Detailed Workplan and Budget. SFEI Contribution No. 1117. San Francisco Estuary Institute: Richmond, California.
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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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Foley, M.; Christian, E.; Goeden, B.; Ross, B. 2020. Expert review of the sediment screening guidelines for the beneficial reuse of dredged material in San Francisco Bay. SFEI Contribution No. 978. San Francisco Estuary Institute: Richmond, CA.

The beneficial reuse of dredged sediment is one strategy in a broader portfolio that is being developed for San Francisco Bay to help marshes adapt to rising sea level. Dredged sediment is currently being used in restoration projects around the Bay, but additional sediment is needed to meet the demand. The guidelines for determining if sediment is appropriate for beneficial reuse were developed twenty years ago. As part of assessing the role of dredged sediment in Bay restoration and adaptation strategies, the Regional Monitoring Program for Water Quality (RMP) and stakeholders recognized the need to revisit the beneficial reuse guidelines for dredged sediment. In September 2019, the RMP convened a workshop that included four technical experts to review the beneficial reuse guidelines. The experts were asked to answer three questions: 1) Are the current screening guidelines appropriate for beneficial reuse? 2) Is the current screening process appropriate and adequate? If not, what are your recommendations for improving it? and 3) How should bioaccumulation potential be addressed for the beneficial reuse of sediment? Based on the discussion of these three questions, six recommendations emerged from the workshop.

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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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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.; 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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Brander, S. M.; Renick, V. C.; Foley, M. M.; Steele, C.; Woo, M.; Lusher, A.; Carr, S.; Helm, P.; Box, C.; Cherniak, S.; et al. 2020. Sampling and Quality Assurance and Quality Control: A Guide for Scientists Investigating the Occurrence of Microplastics Across Matrices. Applied Spectroscopy 74 (9) . SFEI Contribution No. 1012.

Plastic pollution is a defining environmental contaminant and is considered to be one of the greatest environmental threats of the Anthropocene, with its presence documented across aquatic and terrestrial ecosystems. The majority of this plastic debris falls into the micro (1 lm–5 mm) or nano (1–1000 nm) size range and comes from primary and secondary sources. Its small size makes it cumbersome to isolate and analyze reproducibly, and its ubiquitous distribution creates numerous challenges when controlling for background contamination across matrices (e.g., sediment, tissue, water, air). Although research on microplastics represents a relatively nascent subfield, burgeoning interest in questions surrounding the fate and effects of these debris items creates a pressing need for harmonized sampling protocols and quality control approaches. For results across laboratories to be reproducible and comparable, it is imperative that guidelines based on vetted protocols be readily available to research groups, many of which are either new to plastics research or, as with any new subfield, have arrived at current approaches through a process of trial-and-error rather than in consultation with the greater scientific community. The goals of this manuscript are to (i) outline the steps necessary to conduct general as
well as matrix-specific quality assurance and quality control based on sample type and associated constraints, (ii) briefly review current findings across matrices, and (iii) provide guidance for the design of sampling regimes. Specific attention is paid to the source of microplastic pollution as well as the pathway by which contamination occurs, with details provided regarding each step in the process from generating appropriate questions to sampling design and collection.

Zi, T.; Mckee, L.; Yee, D.; Foley, M. 2021. San Francisco Bay Regional Watershed Modeling Progress Report, Phase 1. SFEI Contribution No. 1038. 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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Zi, T.; Braud, A.; McKee, L. J.; Foley, M. 2022. San Francisco Bay Watershed Dynamic Model (WDM) Progress Report, Phase 2. SFEI Contribution No. 1091. San Francisco Estuary Institute: Richmond, California.

The San Francisco Bay total maximum daily loads (TMDLs) call for a 50% reduction in mercury (Hg) loads by 2028 and a 90% reduction in PCBs loads by 2030. In support of these TMDLs, the Municipal Regional Permit for Stormwater (MRP) (SFBRWQCB, 2009, SFBRWQCB, 2015, SFBRWQCB, 2022) called for the implementation of control measures to reduce PCBs and Hg loads from urbanized tributaries. In addition, the MRP has identified additional information needs associated with improving understanding of sources, pathways, loads, trends, and management opportunities of pollutants of concern (POCs). In response to the MRP requirements and information needs, the Small Tributary Loading Strategy (STLS) was developed, which outlined a set of management questions (MQs) that have been used as the
guiding principles for the region’s stormwater-related activities. In recognition of the need to evaluate changes in loads or concentrations of POCs from small tributaries on a decadal scale, the updated 2018 STLS Trends Strategy (Wu et al., 2018) prioritized the development of a new dynamic regional watershed model for POCs (PCBs and Hg focused) loads and trends. This regional modeling effort will provide updated estimates of POC concentrations and loads for all local watersheds that drain to the Bay. The Watershed Dynamic Model (WDM) will also provide
a mechanism for evaluating the impact of management actions on future trends of POC loads or concentrations.

As a multi-use modeling platform, the WDM is being developed to include other pollutants, such as contaminants of emerging concern (CECs), sediment, and nutrients and to be coupled with a Bay fate model to form an integrated watershed-Bay modeling framework to address Regional Monitoring Program (RMP) management questions. As this model is developed, flexibility to link with other models will be an important consideration.

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Ellisor, D.; Buzby, N.; Weaver, M.; Foley, M.; Pugh, R. 2021. The San Francisco Estuary Institute Collection at the NIST Biorepository. NIST Interagency/Internal Report (NISTIR) - 8370. SFEI Contribution No. 1039. National Institute of Standards and Technology: Gaithersburg, MD.

The National Institute of Standards and Technology (NIST) has been collaborating with the San Francisco Bay Estuary Institute (SFEI) since 2009, providing biobanking services at the NIST Biorepository in Charleston, South Carolina in support of their ongoing water quality monitoring program, the Regional Monitoring Program for Water Quality in the San Francisco Bay (RMP). Specimens (bivalve tissue, bird egg contents, fish tissue and sediment) are collected and processed by SFEI-partnering institutions according to their established protocols and shipped to the NIST Biorepository for archival. This report outlines NIST's role in the project, describes collection and processing protocols developed by SFEI and their collaborators, details shipping and archival procedures employed by biorepository staff and provides an inventory of the collection maintained by NIST from 2009 to 2020.

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Mckee, L.; Lowe, J.; Dusterhoff, S.; Foley, M.; Shaw, S. 2020. Sediment Monitoring and Modeling Strategy. Sediment Monitoring and Modeling Strategy. SFEI Contribution No. 1016. San Francisco Estuary Institute: Richmond, CA.
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