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Mercury Effects, Sources, and Control Measures. SFEI Contribution No. 20. San Francisco Estuary Institute: Richmond, CA.
1996. 
Mercury in biosentinel fish in San Francisco Bay: First-year project report. SFEI Contribution No. 520.
2006. 
Mercury in San Francisco Bay forage fish. San Francisco Estuary Institute: Oakland, Ca.
2010. 
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.
2002. Mercury-Selenium Effects on Reproductive Success of Forster's Terns in San Francisco Bay. USGS: Davis, California. p 26.
2009. 
Methods and Data for Analysis of Potential Distribution and Abundance of Zebra Mussels in California. SFEI Contribution No. 225. A report for CALFED and the California Urban Water Agencies. San Francisco Estuary Institute: Richmond CA.
1998. 
Methods for Analysis of Spatial and Temporal Patterns. SFEI Contribution No. 18. San Francisco Estuary Institute: Richmond, CA.
1996. 
Microbial Water Quality at Minimally Human-Impacted Reference Beaches in Northern California. SFEI Contribution No. 858. San Francisco Estuary Institute : Richmond, CA.
2018. 
Microplastic Monitoring and Science Strategy for San Francisco Bay. SFEI Contribution No. 798. San Francisco Estuary Institute: Richmond, Calif.
2017. 
Microplastic Strategy Update. SFEI Contribution No. 951. San Francisco Estuary Institute: Richmond, CA.
2019. Based on the detection of microplastics in San Francisco Bay surface water and Bay Area wastewater effluent in 2015, the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) convened a Microplastic Workgroup (MPWG) in 2016 to discuss the issue, identify management information needs and management questions (MQs), and prioritize studies to provide information to answer these management questions. The MPWG meets annually to review on-going microplastic projects and to conduct strategic long-term planning in response to new information in this rapidly evolving field.
In this nascent field with new findings published almost daily, the Strategy is designed to be a living document that is updated periodically. This Strategy Update includes a short summary of recent findings from the San Francisco Bay Microplastics Project - a major monitoring effort in the Bay - and an updated multi-year plan based on the newly acquired knowledge and current management needs.

Mission Bay Historical Ecology Reconnaissance Study: Data Collection Summary (Technical Report). SFEI Contribution No. 777.
2016. The goals of the Mission Bay Historical Ecology Reconnaissance Study were to collect and compile high-priority historical
data about the Mission Bay landscape, identify sources that could help to develop a deeper understanding of early
ecological conditions, and to identify future possible research directions based on the available data. This technical
memorandum is intended to document the archives consulted during the reconnaissance study, summarize the collected
and compiled data, and to identify potential next steps. A separate technical presentation to project staff and advisors will
summarize the preliminary findings and questions generated from a review of the historical dataset. Ultimately, this
research is intended to support the San Diego Audubon Society’s Mission Bay Wetlands Conceptual Restoration Plan (CRP)
and the ReWild Mission Bay project.

2003.
Model Development Plan to Support Nutrient Management Decisions in San Francisco Bay. SFEI Contribution No. 705. Richmond, CA.
2014. 
Modeling mercury bioaccumulation in largemouth bass in the Sacramento-San Joaquin River Delta and tributaries. SFEI: Oakland, CA. p 22.
2008. 
A Model of Long-Term PCB Fate in San Francisco Bay. San Francisco Estuary Institute: Oakland.
2008. 
Monitoring and Results for El Cerrito Rain Gardens. San Francisco Estuary Institute: Richmond, CA.
2012. 
Monitoring for Non-indigenous Organisms. SFEI Contribution No. 385. San Francisco Estuary Institute: Oakland, CA.
1998. 
Monitoring of Toxic Contaminants in the San Francisco Bay-Delta: A Critical Review. SFEI Contribution No. 152.
1988. Monitoring of Toxic Contaminants in the San Francisco Bay-Delta: A Critical Review, Emphasizing Spatial and Temporal Trend Monitoring. SFEI Contribution No. 153. AHI: Richmond, CA. p 244.
1988. 
Monitoring Plan Petaluma River Watershed Nutrient and Bacteria Impairment Study: Employing the Reachwide Benthos Method for Stream Algae Sampling and Additional Water Column Nutrient and Fecal Indicator Bacteria Measures. Aquatic Science Center: Oakland, CA.
2010. 
Monitoring the US West Coast: An Assessment of California’s Estuaries and the Pacific Ocean:Spatial Hierarchy and its Rationale. SFEI Contribution No. 120. San Francisco Estuary Institute: Oakland, CA.
2002. 
Monitoring Trace Organic Contamination in Central Valley Fish: Current Data and Future Steps. SFEI Contribution No. 99. San Francisco Estuary Institute: Oakland, CA.
2004. 
Mt. Wanda Historical Ecology Investigation. SFEI Contribution No. 743. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 51.
2015. 

Napa River Sediment TMDL Baseline Study: Geomorphic Processes and Habitat form and function in Soda Creek. SFEI Contribution No. 63. San Francisco Estuary Institute: Oakland, CA.
2002. 
Napa River Watershed Profile: Past and Present Characteristics with Implications for Future Management of the Changing Napa River Valley. San Francisco Estuary Institute: Richmond, CA. p 172.
2012. 
Natural Flow Hydrodynamic Modeling Technology Support Phase 1 Technical Memorandum.
2014. This technical memorandum summarizes the work to date carried out by the San Francisco Estuary Institute (SFEI) to generate a bathymetric-topographic digital elevation model (DEM) of the historical Sacramento-San Joaquin Delta (representative of early 1800s conditions). The historical DEM described in this document is an interim/draft product completed for Phase I of the Bay-Delta Natural Flow Hydrodynamics and Salinity Transport modeling project. It is expected that the product and methods described here will be refined during a second phase of the project.

Newcomb Avenue Green Street (Case Study Site and Technical Reports). SFEI Contribution No. 793.
2014. 

Nonindigenous Aquatic Species in a United States Estuary: A Case Study of the Biological Invasions of the San Francisco Bay and Delta. U. S. Fish and Wildlife Service: Washington DC.
1995. Non-Targeted Analysis of Water-Soluble Compounds Highlights Overlooked Contaminants and Pathways (Coming Soon). SFEI Contribution No. 905. San Francisco Estuary Institute: Richmond, CA.
2018. North Bay Mercury Biosentinel Project: 2016 - 2017. SFEI Contribution No. 868.
2018. 
North Bay Mercury Biosentinel Project (December 2014 Report). SFEI Contribution No. 738. San Francisco Estuary Institute: Richmond, CA.
2014. 
North Bay Selenium Monitoring Design. SFEI Contribution No. 921. San Francisco Estuary Institute : Richmond, CA.
2018. 
Northern San Diego County Lagoons Historical Ecology Investigation. SFEI Contribution No. 722. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 215.
2014. 

Novato Creek Baylands Historical Ecology Study. SFEI Contribution No. 740. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.
2015. Project Background
Over the past century and a half, lower Novato Creek and the surrounding tidal wetlands have been heavily modified for flood control and land reclamation purposes. Levees were built in the tidal portion of the mainstem channel beginning in the late 1800s to convey flood flows out to San Pablo Bay more rapidly and to remove surrounding areas from inundation. Following levee construction, the wetlands surrounding the channel were drained and converted to agricultural, residential, and industrial areas. These changes have resulted in a considerable loss of wetland habitat, reduced sediment transport to marshes and the Bay, and an overall decreased resilience of the system to sea level rise.
In addition to tidal wetland modification, land use changes upstream in the Novato Creek watershed have resulted in several challenges for flood control management. Dam construction and increased runoff in the upper watershed have resulted in elevated rates of channel incision, which have increased transport of fine sediment from the upper watershed to lower Novato Creek. Channelization of tributaries and construction of irrigation ditches have likely increased drainage density in the upper watershed, also potentially contributing to increased rates of channel incision and fine sediment production (Collins 1998). Downstream, sediment transport capacity has been reduced by construction of a railroad crossing and loss of tidal prism and channel capacity associated with the diking of the surrounding marsh. As a result of the increased fine sediment supply from the watershed and the loss of sediment transport capacity in lower Novato Creek, sediment aggradation occurs within the channel, which in turn reduces the flood capacity of the channel, necessitating periodic dredging.
Currently, the Marin County Department of Public Works (MCDPW) is coordinating the Novato Watershed Program, which includes Marin County Flood Control and Water Conservation District, Novato Sanitary District, and North Marin Water District. Within lower Novato Creek, the Program is seeking to implement a new approach to flood control that includes redirecting sediment for beneficial use, reducing flood channel maintenance costs, restoring wetland habitat, and enhancing resilience to sea level rise. Included as part of this goal is the re-establishment of historical physical processes that existed before major channel modification, which in turn will re-establish historical ecological functions and help to create a tidal landscape that is resilient to increasing sea level.

Novato Creek Baylands Vision: Integrating ecological functions and flood protection within a climate-resilient landscape. SFEI Contribution No. 764.
2015. This report explores the potential for integrating ecological functions into flood risk management on lower Novato Creek. It presents an initial vision of how ecological elements could contribute to flood protection, based on a broad scale analysis and a one day workshop of local and regional experts. The Vision is not intended to be implemented as is, but rather adapted and applied through future projects and analysis. Other actions (e.g., floodwater detention basins) may also need to be implemented in the interim to meet flood risk objectives.

Nutrient Management Strategy Science Plan Report. SFEI Contribution No. 878. San Francisco Estuary Institute: Richmond, CA.
2016. 
Nutrient Management Strategy Science Program. SFEI Contribution No. 879. San Francisco Estuary Institute: Richmond, CA.
2017. 
Nutrient Monitoring Planning Workshop - Summary of Existing Nutrient Monitoring Programs, Data Gaps, and Potential Delta RMP “No Regrets” Monitoring Activities. Aquatic Science Center: Richmond, CA.
2016. This report was prepared as a briefing document for a September 2016 workshop held in Sacramento by the Delta Regional Monitoring Program. The purpose of the workshop was to plan how to invest in nutrients-related studies in order to inform better management of Delta waterways. First, the report compiles information about the major existing nutrient monitoring programs in the Sacramento-San Joaquin Delta. Next, it outline options for “no regrets” actions for workshop participants to review. The report summarizes interviews with representatives of Delta monitoring and resource management programs, describes current monitoring efforts in the Delta, and presents the conclusions and recommendations from recently completed data syntheses.
Nutrient Moored Sensor Program: Year 1 Progress Update. SFEI: Richmond, CA.
2014. 
Nutrient Stormwater Monitoring Results: WY2012 and WY2013. San Francisco Estuary Institute: Richmond, CA.
2014. 
Observational Study of Sycamore Regeneration at two sites in Santa Clara County after the 2016-2017 Water Year. SFEI Contribution No. 874.
2018. 
Observations on trace organic concentrations in RMP water samples. SFEI Contribution No. 210. San Francisco Estuary Institute. pp 67-77.
1997. Ohio Rapid Assessment Method for Wetlands v. 5.0 Users Manual and Scoring Forms. State of Ohio Environmental Protection Agency: Ohio. p 107.
. 2001. Online 401: From Pilot to Production. San Francisco Estuary Institute: Richmond, CA.
2014. 
Optimizing sampling methods for pollutant loads and trends in San Francsico Bay urban stormwater monitoring. San Francisco Estuary Institute: Oakland, CA.
2010. 
Optimizing Transplanted Bivalve Studies for the Regional Monitorig Program for Trace Substances. . SFEI Contribution No. 431. San Francisco Estuary Institute.
2005. 
Organochlorine Pesticide Fate in San Francisco Bay. SFEI Contribution No. 433. San Francisco Estuary Institute: Oakland, CA. p 48.
2006. 
Overview of 2004/05 Rapid Assessment Shore and Channel Surveys for Exotic Species in San Francisco Bay. SFEI Contribution No. 452. San Francisco Estuary Institute: Oakland, CA.
2005. 
1999.
1998.
Pathogen Occurrence and Analysis in Relation to Water Quality Attainment in San Francisco Bay Area Watersheds. SFEI Contribution No. 128.
2002. 
Patterns of Water-Quality Variability in San Francisco Bay During the First Six Years of the RMP, 1993-1998. SFEI Contribution No. 41. San Francisco Estuary Institute: Richmond, CA.
2000. 
A PCB Budget for San Francisco Bay. SFEI Contribution No. 376. San Francisco Estuary Institute: Oakland, CA.
2002. PCB intercalibration exercise with Regional Monitoring Program water sample extracts. SFEI Contribution No. 204. San Francisco Estuary Institute: Richmond, CA. pp 234-239.
1997. PCBs in effluent. SFEI Contribution No. 237.
2001. PCBs in San Francisco Bay: Assessment of the Current State of Knowledge and Priority Information Gaps. SFEI Contribution No. 727. SFEI: Richmond, CA.
2014. 
Pelagic Organism Decline. SFEI Contribution No. 511.
2005. Per and Polyfluoroalkyl Substances (PFAS) in San Francisco Bay: Synthesis and Strategy. SFEI Contribution No. 867. San Francisco Estuary Institute : Richmond, CA.
2018. 
Petaluma River Impairment Assessment for Nutrients, Sediment/Siltation, and Pathogens Part 1: Existing Information and TMDL Comparison. Aquatic Science Center: Oakland.
2010. 
Petaluma Valley Historical Hydrology and Ecology Study. SFEI Contribution No. 861. San Francisco Estuary Institute: Richmond, CA.
2018. This study reconstructs the historical landscape of the Petaluma River watershed and documents the major landscape changes that have taken place within the watershed over the past two centuries. Prior to Spanish and American settlement of the region, the Petaluma River watershed supported a dynamic and interconnected network of streams, riparian forests, freshwater wetlands, and tidal marshes. These habitats were utilized by a wide range of plant and animal species, including a number of species that are today listed as threatened or endangered such as Ridgway’s Rail, Black Rail, salt marsh harvest mouse, California red-legged frog, Central California Coast steelhead, and soft bird’s beak (CNDDB 2012, SRCD 2015). Agricultural and urban development beginning in the mid-1800s has significantly altered the landscape, degrading habitat for fish and wildlife and contributing to contemporary management challenges such as flooding, pollutant loading, erosion, and sedimentation. While many natural areas and remnant wetlands still exist throughout the watershed—most notably the Petaluma Marsh—their ecological function is in many cases seriously impaired and their long-term fate jeopardized by climate change and other stressors. Multi-benefit wetland restoration strategies, guided by a thorough understanding of landscape history, can simultaneously address a range of chronic management issues while improving the ecological health of the watershed, making it a better place to live for both people and wildlife.


Pharmaceuticals and Personal Care Products in Wastewater Treatment Plant Influent and Effluent and Surface Waters of Lower South San Francisco Bay. San Francisco Estuary Institute: Oakland, Ca.
2009. Phase 2 (2003) Bioassessment of Waterbodies Treated with Aquatic Pesticides. SFEI Contribution No. 117. San Francisco Estuary Insitute: Oakland, CA.
2004. 
Pilot Study Examining Spatial Differences in Water Quality Between Shoal and Channel Habitats. SFEI Contribution No. 948. San Francisco Estuary Institute: Richmond, CA.
2019. 
Pilot Study of Contaminants of Emerging Concern (CECs) in the Russian River Watershed: Lessons Learned. SFEI Contribution No. 852. San Francisco Estuary Institute: Richmond, CA.
2017. 
A Pilot Study of the Effects of Contaminants on surfperch (Cymatogaster aggregata) in the San Francisco Bay Estuary. San Francisco Estuary Institute.
2007. 
Pinole Creek Sediment Source Assessment: Pavon Creeks Sub-basin. SFEI Contribution No. 515. San Francisco Estuary Institute. p 67.
2006. 

Pinole Creek Watershed Sediment Source Assessment. A technical report of the Regional Watershed Program, San Francisco Estuary Institute (SFEI), Oakland, California. (report only -- no appendix). SFEI Contribution No. 316. San Francisco Estuary Institute: Oakland, CA.
2005. 
Pinole Creek Watershed Sediment Source Assessment. A technical report of the Regional Watershed Program, San Francisco Estuary Institute (SFEI), Oakland, California. (appendix only). SFEI Contribution No. 316. San Francisco Estuary Institute: Oakland, CA.
2005. 
Pollutant Monitoring in the North Richmond Pump Station: A Pilot Study for Potential Dry Flow and Seasonal First Flush Diversion for Wastewater Treatment. San Francisco Estuary Institute: Richmond, CA.
2012. 
Pollutants of concern (POC) loads monitoring data progress report, water year (WY) 2012. SFEI: Richmond, CA.
2013. 
Pollutants of Concern (POC) Loads Monitoring Data Progress Report: Water Years (WYs) 2012 and 2013. SFEI Contribution No. 708. SFEI: Richmond, CA. pp 1-84.
2014. 
Pollutants of Concern (POC) Loads Monitoring Data, Water Year (WY) 2011. San Francisco Estuary Institute: Richmond, CA.
2012. 
Pollutants of concern (POC) loads monitoring progress report, water years (WYs) 2012, 2013, and 2014. SFEI Contribution No. 741.
2016. 
Pollutants of concern (POC) reconnaissance monitoring final progress report, water year (WY) 2015. SFEI Contribution No. 787.
2016. 
Pollutants of concern reconnaissance monitoring final progress report, water years 2015 and 2016. SFEI Contribution No. 817.
2017. 
Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2018. SFEI Contribution No. 942. San Francisco Estuary Institute: Richmond, CA.
2019. 
Pollutants of Concern Reconnaissance Monitoring Water Years 2015, 2016, and 2017. SFEI Contribution No. 840. San Francisco Estuary Institute: Richmond, CA.
2018. 
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.
2014. 
Polychlorinated Biphenyls in Northern San Francisco Estuary Refinery Effluents. SFEI Contribution No. 510.
2002. Potential biological indicators of contaminant effects for use in monitoring the San Francisco Estuary. SFEI Contribution No. 43. San Francisco Estuary Institute.
2001. The Potential Distribution and Abundance of Zebra Mussels in California. SFEI Contribution No. 225. San Francisco Estuary Institute: Richmond, CA.
1998. 
The Potential Distribution of Chinese Mitten Crabs (Eriocheir sinensis) in selected waters of the Western United States with U.S. Bureau of Reclamation Facilities. SFEI Contribution No. 353. United States Department of the Interior, Bureau of Reclamation, Mid-Pacific Region and the Technical Service Center. Vol. 21.
2001. 
Potential Distribution of Zebra Mussels (Dreissena polymorpha) and Quagga Mussels (Dreissena bugensis) in California Phase 1 Report. A Report for the California Department of Fish and Game. San Francisco Estuary Institute.
2007. 
Potential Introduction of Nonindigenous Species to Prince William Sound, Alaska Via Discharge of Tanker Ballast Water. A report for B. P. Exploration (Alaska) Inc.: Anchorage, AK.
1996. Power Analysis and Optimization of the RMP Status and Trends Program. SFEI Contribution No. 555.
2008. 
Practical Guidebook to the Control of Invasive Aquatic and Wetland Plants of the San Francisco Bay - Delta Region. SFEI Contribution No. 127. San Francisco Estuary Institute.
2003. Preliminary Simulations of Sediment Dynamics in the South San Francisco Bay. San Francisco Estuary Institute: Oakland, CA.
2011. 
Presence of marine invasive species along the coast of Massachusetts. SFEI Contribution No. 509.
2002. Primary Production in the Sacramento-San Joaquin Delta: A Science Strategy to Quantify Change and Identify Future Potential. SFEI Contribution No. 781.
2016. 
Procedures for the Collection and Storage of Environmental Samples in the RMP Specimen Bank. San Francisco Estuary Institute: Oakland, CA.
2010. 
Project Report: 2004 Rapid Assessment Survey for Exotic Species in San Francisco Bay. SFEI Contribution No. 451. San Francisco Estuary Institute: Oakland, Ca.
2005. Project Report for the Southern California Exotics Expedition 2000 A Rapid Assessment Survey of Exotic Species in Sheltered Coastal Waters. SFEI Contribution No. 384. San Francisco Estuary Institute: Oakland.
2002. 
Project Report for the Southern California Exotics Expedition 2000: A Rapid Assessment Survey of Exotic Species in Sheltered Coastal Waters. Appendix C in:. . California Department of Fish and Game, Office of Oil Spill Prevention and Response, Sacramento CA.
2001.