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Book Chapter
Davis, J. A. 2000. Chlorinated Hydrocarbons in the San Francisco Estuary and its Watershed. In Draft Chapter in Spies, R.B. (ed.). Contaminants and Toxicity in the Sacramento-San Joaquin Delta, Its Cathchment, and the San Francisco Estuary - A CALFED White Paper. Applied Marine Sciences, Livermore, CA.. Draft Chapter in Spies, R.B. (ed.). Contaminants and Toxicity in the Sacramento-San Joaquin Delta, Its Cathchment, and the San Francisco Estuary - A CALFED White Paper. Applied Marine Sciences, Livermore, CA.
Collins, J. N.; Schwarzbach, S. E.; Luoma, S. N.; Yee, D.; Davis, J. A. 2000. Mercury and tidal wetland restoration. In Chapter 6 in Brown, L. (ed.). DRAFT CALFED Whitepaper on: Ecological Processes in Tidal Wetlands of the Sacramento-San Joaquin Estuary and Their Implications for Proposed Restoration Efforts of the Ecosystem Restoration Program.. Chapter 6 in Brown, L. (ed.). DRAFT CALFED Whitepaper on: Ecological Processes in Tidal Wetlands of the Sacramento-San Joaquin Estuary and Their Implications for Proposed Restoration Efforts of the Ecosystem Restoration Program.
Davis, J. A.; Richardson, C. J. 1987. Natural and artificial wetland ecosystems - ecological opportunities and limitations. In Aquatic Plants for Water Treatment and Resource Recovery. K.R., R., Smith, W. H., Eds.. Aquatic Plants for Water Treatment and Resource Recovery. University of Florida: Gainesville, FL.
Conference Proceedings
Connor, M. S.; Davis, J. A. 2008. The State of San Francisco Bay: Water Quality. National Water Quality Monitoring Conference.
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Journal Article (Peer-Reviewed)
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Davis, J. A. 2004. The Long-Term Fate of PCBs in San Francisco Bay. Environmental Toxicology and Chemistry 23, 2396-2409.
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Collins, J. N.; Yee, D.; Davis, J. A. 2002. Mercury and tidal wetland restoration. CalFED Journal . SFEI Contribution No. 339.
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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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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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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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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.

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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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Magazine Article
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Miscellaneous
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Report
Lowe, S.; Hoenicke, R.; Davis, J. A. 1999. 1999 Quality Assurance Project Plan. SFEI Contribution No. 33. San Francisco Esturary Institute: Oakland.
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Davis, J. A.; SFEI. 2006. 2006 Pulse of the Estuary: Monitoring and Managing Water Quality in the San Francisco Estuary. SFEI Contribution No. 517. San Francisco Estuary Institute: Oakland, CA. p 82.
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Davis, J. A. 2014. 2014 Regional Monitoring Program Update. SFEI Contribution No. 728. San Francisco Estuary Institute: Richmond, CA.
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Salop, P.; Shimabuku, I.; Davis, J.; Franz, A. 2018. 2018 Bivalve Retrieval Cruise Report. SFEI Contribution No. 920. San Francisco Estuary Institute : Richmond, CA.
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Davis, J. 2018. 2018 Regional Monitoring Program Update. SFEI Contribution No. 906. San Francisco Estuary Institute : Richmond, CA.
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Trowbridge, P.; Wong, A.; Davis, J.; Ackerman, J. 2018. 2018 RMP Bird Egg Monitoring Sampling and Analysis Plan. SFEI Contribution No. 891. San Francisco Estuary Institute: Richmond, CA.
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Foley, M.; Davis, J.; Yee, D. 2019. 2019 RMP Annual Workplan and Budget. San Francisco Estuary Institute: Richmond, CA.

In 2019 the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is entering its 27th year of collecting data and communicating information to support water quality management decisions. This Detailed Workplan and Budget describes the activities that will be completed in 2019, the proposed funding levels, and the deliverables for each task.

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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.; Davis, J.; Yee, D. 202AD. 2022 RMP Detailed Workplan and Budget. SFEI Contribution No. 1183. San Francisco Estuary Institute: Richmond, CA.

In 2022 the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is entering its 31st year of collecting data and communicating information to support water quality management decisions. This Detailed Workplan and Budget describes the activities that will be completed in 2022, the proposed funding levels, and the deliverables for each task.In 2022 the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is entering its 31st year of collecting data and communicating information to support water quality management decisions. This Detailed Workplan and Budget describes the activities that will be completed in 2022, the proposed funding levels, and the deliverables for each task.

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Mendez, M.; Kleckner, A.; Sutton, R.; Yee, D.; Wong, A.; Davis, J.; Sigala, M. 2023. 2023 Bay Prey Fish and Near-field / Margins Sediment Sampling and Analysis Plan. SFEI Contribution No. 1141. San Francisco Estuary Institute: Richmond, CA.

This is a sampling and analysis plan for the Bay Status and Trends (S&T) Prey Fish and Near-field / Margins Sediment monitoring for the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). Bay margins are defined by the RMP as extending from Mean Higher High Water (MHHW) to 1 foot below Mean Lower Low Water (MLLW). These mud flats and adjacent shallow areas of the Bay are productive and highly utilized by biota of interest (humans and wildlife). Near-field stations are located near watershed inputs in the Bay. Prey fish are a key matrix to monitoring the status and impacts of contaminants, especially near margin areas where they have shown strong contamination signals in previous RMP studies. This monitoring design provides a spatially-distributed characterization of contaminant concentrations in fish and sediment found within the margins of Central Bay, South Bay, and Lower South Bay. This study builds on previous S&T efforts to characterize surface sediment contamination across the Bay while piloting routine monitoring of prey fish. Additional samples outside of S&T will be collected for special studies. A subset of samples will be archived for potential future analysis of emerging contaminants or other analyte groups.

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Kleckner, A.; Sutton, R.; Yee, D.; Wong, A.; Davis, J.; Salop, P. 2023. 2023 RMP Dry Season Water Cruise Plan. SFEI Contribution No. 1139. San Francisco Estuary Institute: Richmond, CA.

This report details plans associated with the 2023 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 stations in place of the twenty-six base program stations sampled previously. In 2007, the number of stations was decreased to twenty-two stations, and it remains as such for 2023. The analytes for 2023 are based on the Status and Trends (S&T) Review process that started in 2020.

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