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 ?13C and ?15N were similar for the USGS and RMP samples with ?13C and ?15N 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.

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. 

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.

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.

Davis, J. A.; Gilbreath, A. N. 2019. Small Tributaries Pollutants of Concern Reconnaissance Monitoring: Pilot Evaluation of Source Areas Using PCB Congener Data.  SFEI Contribution No. 956. San Francisco Estuary Institute: Richmond, CA.

McKee, L. J.  .; Gilbreath, A. N.; Hunt, J. A.; Wu, J.; Yee, D.; Davis, J. A. 2019. Small Tributaries Pollutants of Concern Reconnaissance Monitoring: Loads and Yields-based Prioritization Methodology Pilot Study.  SFEI Contribution No. 817. San Francisco Estuary Institute: Richmond, CA.

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.

Melwani, A.; Yee, D.; McKee, L.; Gilbreath, A.; Trowbridge, P.; Davis, J. 2018. Statistical Methods Development and Sampling Design Optimization to Support Trends Analysis for Loads of Polychlorinated Biphenyls from the Guadalupe River in San Jose, California, USA.  SFEI Contribution No. 876. Applied Marine Sciences: Livermore, CA.

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.

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.

Sun, J.; Robinson, A.; Davis, J. A.; Trowbridge, P.; A. Stewart, R.; Palace, V. P.; Jackson, Z. J. 2017. Selenium in White Sturgeon Tissues: 2015 Sturgeon Derby.  SFEI Contribution No. 834.

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.

Sun, J.; Robinson, A.; Davis, J. A. 2016. Selenium in Sturgeon Muscle Plugs: 2014.

Yee, D.; Davis, J. A.; Gilbreath, A. N.; McKee, L. J. 2016. Simple Mass Budget Model to Evaluate Long Term PCB Fate in the Emeryville Crescent Sub-embayment.

Trowbridge, P.; Senn, D. B.; Yee, D.; Novick, E.; Davis, J. A. 2014. San Francisco Bay Nutrient Management Strategy: Detailed Modeling Workplan for FY15-FY21. San Francisco Estuary Institute: Richmond, CA.

Davis, J. A.; Schiff, K.; Melwani, A. R.; Bezalel, S. N.; Hunt, J. A.; Allen, R.; Ichikawa, G.; Bonnema, A.; Heim, W.; Crane, D.; et al. 2011. SWAMP/RMP/Bight Program Report on Contaminants in Fish from the California Coast. California State Water Resources Control Board: Sacramento, CA.

Eagles-Smith, C.; Hunt, J.; Ackerman, J.; Davis, J. A.; Sedlak, M. 2009. San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants - 2009 Data Summary. U. S. Geological Survey: Davis, CA.

Melwani, A. R.; Bezalel, S. N.; Hunt, J. A.; Grenier, J. Letitia; Ichikawa, G.; Heim, W.; Bonnema, A.; Foe, C.; Slotton, D. G.; Davis, J. A. 2009. Spatial trends and impairment assessment of mercury in sport fish in the Sacramento-San Joaquin Delta Watershed. Environmental Pollution . SFEI Contribution No. 575.

Davis, J. A.; Lowe, S.; Hoenicke, R. 2008. Science Support for the Surface Water Ambient Monitoring Program, SWRCB Agreement No. 03-200-250-0.  SFEI Contribution No. 546. San Francisco Estuary Institute.

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.

Connor, M.; Flegal, A. R.; Davis, J. A. 2008. The State of San Francisco Bay: Water Quality.

Connor, M. S.; Davis, J. A. 2008. The State of San Francisco Bay: Water Quality. National Water Quality Monitoring Conference.

Davis, J. A. 2008. SWAMP Fact Sheet: Long-Term Monitoring of Pollutants in Fish and Mussels Documents Major Improvements and Persistent Problems.

Oram, J. J.; Greenfield, B. K.; Davis, J. A.; Werme, C.; Connor, M. S.; Gunther, A.; Hardin, D.; Mumley, T.; Leatherbarrow, J. E. 2007. The slow recovery of the San Francisco Estuary from the legacy of organochlorine pesticides. Environmental Pollution . SFEI Contribution No. 488.

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.

Davis, J. A.; Connor, M. S.; Flegal, A. R. 2007. The State of San Francisco Bay: Water Quality.

Hunt, J. A.; Davis, J. A.; Lowe, S.; Crane, D.; Ross, J. R. M.; Lovvom, J.; Burkholder, B. 2006. Selenium Concentrations in Surt Scoter.

Greenfield, B. K.; Davis, J. A.; Fairey, R.; Crane, D.; Ichikawa, G.; Roberts, C. 2004. Seasonal, Interannual, and Long-term Variation in sport fish contamination, San Francisco Bay. Science of the Total Environment . SFEI Contribution No. 81.

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.

Greenfield, B. K.; Davis, J. A. 2004. Sport fish contamination in the Bay-Delta watershed.

McKee, L. J.  .; Davis, J. A.; Ganju, N.; Shellenbarger, G.; Schoellhamer, D. H. 2003. Sediment Dynamics Drive Contaminant Dynamics.

Davis, J. A.; Lowe, S.; Hunt, J. A.; Crane, D.; Ross, J. R. M.; Lovvom, J.; Burkholder, B. 2003. Selenium Concentrations in Surf Scooter and Greater Scaup from the San Francisco Estuary.

Davis, J. A.; Lowe, S.; Anderson, B.; Phillips, B. M.; Hunt, J. A.; Tjeerdema, R. S.; Taberski, K.; Thompson, B.; Nicely, P. 2003. Summary of 10 years of sediment toxicity monitoring for the San Francisco Estuary RMP.  SFEI Contribution No. 281. San Francisco Estuary Institute.

Lowe, S.; David, N.; Oros, D. R.; Jarman, W. M.; Lowe, T.; Davis, J. A. 2003. Surveillance for previously unmonitored organic contaminants in the San Francisco Estuary. Marine Pollution Bulletin 46, 1102-1110 . SFEI Contribution No. 295.

Lowe, S.; David, N.; Oros, D. R.; Jarman, W. M.; Lowe, T.; Davis, J. A. 2003. Surveillance for previously unmonitored organic contaminants in the San Francisco Estuary. Marine Pollution Bulletin 46, 1102-1110.

Davis, J. A.; Lowe, S.; David, N.; Oros, D. R.; Jarman, W. M.; Lowe, T. 2003. Surveillance for previously unmonitored organic contaminants in the San Francisco Estuary. Marine Pollution Bulletin 46 (9), 1102-10 . SFEI Contribution No. 469.

Davis, J. A.; Collins, J. N.; May, M. 2002. Sediment Contaminants.

Greenfield, B. K.; Davis, J. A.; Fairey, R.; Crane, D.; Stephenson, M.; Roberts, C.; Ichicawa, G. 2001. Seafood Contamination and Consumption.

Davis, J. A.; Yee, D.; Leatherbarrow, J. E. 2001. South Bay/Fairfield-Suisun Trace Organic Contaminants in Effluent Study.  SFEI Contribution No. 236. p 53.

Davis, J. A.; Gunther, A.; O'Connor, J. M.; Spies, R. B.; Richardson, B. J.; Wyatt, E.; Larson, E.; Meiorin, E. C. 1991. San Francisco Estuary Project Status and Trends Report on Pollutants in the San Francisco Estuary, Final Draft.  SFEI Contribution No. 162. AHI: Richmond, CA. p 291.

Gunther, A. J.; O'Connor, J. M.; Spies, R. B.; Richardson, B. J.; Wyatt, E.; Larson, E.; Davis, J. A. 1991. Status and Trends Report on Pollutants in the San Francisco Estuary.  SFEI Contribution No. 161. San Francisco Estuary Project: Oakland, CA.

Gunther, A. J.; O'Connor, J. M.; Spies, R. B.; Richardson, B. J.; Wyatt, E.; Larson, E.; Meiorin, E. C.; Davis, J. A. 1991. Status and Trends Report on Pollutnats in the San Francisco Estuary. San Francisco Bay-Delta Aquatic Habitat Institute: Richmond CA. p 291.

Gunther, A. J.; O'Connor, J. M.; Williams, P. S.; Davis, J. A. 1990. Status and Trends Report on Dredging and Waterway Modification in the San Francisco Estuary.  SFEI Contribution No. 159. San Francisco Estuary Project: Oakland, CA.