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1998.
Pathogen Occurrence and Analysis in Relation to Water Quality Attainment in San Francisco Bay Area Watersheds. SFEI Contribution No. 128.
2002. (133.07 KB)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. (421.66 KB)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. (11.99 MB)PCBs in Shiner Surfperch in Priority Margin Areas of San Francisco Bay. SFEI Contribution No. 1054.
2021. (7.81 MB)Conceptual models developed for selected San Francisco Bay margin areas (referred to as priority margin units, or PMUs) have identified shiner surfperch as a crucial indicator of PCB impairment, due to their explicit inclusion as an indicator species in the PCBs TMDL, importance as a popular sport fish species, tendency to accumulate high PCB concentrations, site fidelity, and other factors. The conceptual models recommend periodic monitoring of shiner surfperch to track trends in the PMUs, and as the ultimate indicator of progress in reduction of impairment. The objectives of this study were to 1) establish baselines for long-term monitoring of PCB concentrations in shiner surfperch in four PMUs, and 2) understand local spatial variation in shiner PCB concentrations to support optimization of the long-term sampling design. This study also provided valuable information on the presence of shiner surfperch and other species in the PMUs.
Pelagic Organism Decline. SFEI Contribution No. 511.
2005. Peninsula Watershed Historical Ecology Study. SFEI Contribution No. 1029. San Francisco Estuary Institute: Richmond, Ca.
2021. (204.95 MB) (21.97 MB)Per and Polyfluoroalkyl Substances (PFAS) in San Francisco Bay: Synthesis and Strategy. SFEI Contribution No. 867. San Francisco Estuary Institute : Richmond, CA.
2018. (3.2 MB)Petaluma River Baylands Strategy. Prepared by San Francisco Estuary Institute, Sonoma Land Trust, Point Blue Conservation Science, Ducks Unlimited, and Sonoma Resource Conservation District. Funded by the Wildlife Conservation Board.
. 2023. (12.81 MB) (12.16 MB)Petaluma River Impairment Assessment for Nutrients, Sediment/Siltation, and Pathogens Part 1: Existing Information and TMDL Comparison. Aquatic Science Center: Oakland.
2010. (1.89 MB)Petaluma River Watershed Contemporary Riparian Condition Assessment. Petaluma River Watershed Contemporary Riparian Condition Assessment. SFEI Contribution No. 1160. San Francisco Estuary Institute: Richmond, CA.
2024. (7.81 MB)Petaluma Valley Historical Hydrology and Ecology Study. SFEI Contribution No. 861. San Francisco Estuary Institute: Richmond, CA.
2018. (121.7 MB) (43.68 MB)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.
PFAS in San Francisco Bay Water. SFEI Contribution No. 1094. San Francisco Estuary Institute: Richmond, CA.
2022. (2.37 MB)Per- and polyfluoroalkyl substances (PFAS), a family of thousands of synthetic, fluorine-rich compounds commonly referred to as “forever chemicals,” are known for their thermal stability, non-reactivity, and surfactant properties. These unique compounds have widespread uses across consumer, commercial, and industrial products, resulting in widespread occurrence in the environment and wildlife across the globe. This study analyzed ambient surface water in San Francisco Bay for 40 PFAS to discern the occurrence, fate, and potential risks to ecological and human health.
Eleven of 40 PFAS were detected in ambient surface water collected in 2021 from 22 sites in the Bay. Seven PFAS (PFPeA, PFHxA, PFHpA, PFOA, PFBS, PFHxS, and PFOS), were found in at least 50% of samples. PFHxA and PFOA were the most frequently detected analytes (detection frequencies of 86% and 77%, respectively). PFPeA and PFHxA were generally found at the highest concentrations across sites, with median and maximum concentrations of 1.6 and 4.8 ng/L and 1.5 and 5.7 ng/L, respectively. Pairwise Spearman's correlations revealed strong positive correlations (p <0.001; r > 0.77) among the seven PFAS detected in at least 50% of sites, suggesting significant similarities between their sources, pathways, and/or fate in the environment. PFBA, PFNA, PFDA, and 6:2 FTS were found at a limited number of sites in the Bay. 6:2 FTS was found at a single site at 14 ng/L, the highest concentration of any individual PFAS in the Bay. The sums of detected PFAS for all sites had median and maximum concentrations of 10 and 29 ng/L, respectively.
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. (577.14 KB)Pilot Study Examining Spatial Differences in Water Quality Between Shoal and Channel Habitats. SFEI Contribution No. 948. San Francisco Estuary Institute: Richmond, CA.
2019. (3.11 MB)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. (796.56 KB)A Pilot Study of the Effects of Contaminants on surfperch (Cymatogaster aggregata) in the San Francisco Bay Estuary. San Francisco Estuary Institute.
2007. (1.62 MB)Pinole Creek Sediment Source Assessment: Pavon Creeks Sub-basin. SFEI Contribution No. 515. San Francisco Estuary Institute. p 67.
2006. (51.71 MB) (25.63 MB)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. (1.29 MB)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. (4.28 MB)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. (1.4 MB)Pollutants of concern (POC) loads monitoring data progress report, water year (WY) 2012. SFEI: Richmond, CA.
2013. (2.33 MB)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. (1.91 MB)Pollutants of Concern (POC) Loads Monitoring Data, Water Year (WY) 2011. San Francisco Estuary Institute: Richmond, CA.
2012. (1.03 MB)Pollutants of concern (POC) loads monitoring progress report, water years (WYs) 2012, 2013, and 2014. SFEI Contribution No. 741.
2016. (2.58 MB)Pollutants of concern (POC) reconnaissance monitoring final progress report, water year (WY) 2015. SFEI Contribution No. 787.
2016. (2.71 MB)Pollutants of concern reconnaissance monitoring final progress report, water years 2015 and 2016. SFEI Contribution No. 817.
2017. (4.01 MB)Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2020. SFEI Contribution No. 1061. San Francisco Estuary Institute: Richmond, CA.
2021. (3.22 MB)The San Francisco Bay polychlorinated biphenyl (PCB) and mercury (Hg) total maximum daily loads (TMDLs) call for implementation of control measures to reduce PCB and Hg loads entering the Bay via stormwater. In 2009, the San Francisco Bay Regional Water Quality Control Board (Regional Water Board) issued the first Municipal Regional Stormwater Permit (MRP). This MRP contained a provision aimed at improving information on stormwater pollutant loads in selected watersheds (Provision C.8.) and piloted a number of management techniques to reduce PCB and Hg loading to the Bay from smaller urbanized tributaries (Provisions C.11. and C.12.). To address C8, a previously developed fixed station loads monitoring technique was refined that incorporated turbidity and stage sensors recording at 5-15 minute intervals with the collection of velocity and water samples using both manual and auto sampling techniques to compute loads. In 2015, the Regional Water Board issued the second iteration of the MRP. “MRP 2.0” placed an increased focus on identifying those watersheds, source areas, and source properties that are potentially the most polluted and are therefore most likely to be cost-effective areas for addressing load-reduction requirements.
Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015 - 2019. SFEI Contribution No. 987. San Francisco Estuary Institute: Richmond, CA.
2020. (1.6 MB)Reconnaissance monitoring for water years 2015, 2016, 2017, 2018 and 2019 was completed with funding provided by the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). This report is designed to be updated each year until completion of the study. At least one additional water year (2020) is underway. An earlier draft of this report was prepared for the Bay Area Stormwater Management Agencies Association (BASMAA) in support of materials submitted on or before March 31st 2020 in compliance with the Municipal Regional Stormwater Permit (MRP) Order No. R2-2015-0049.
Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2018. SFEI Contribution No. 942. San Francisco Estuary Institute: Richmond, CA.
2019. (3.37 MB)Pollutants of Concern Reconnaissance Monitoring Water Years 2015, 2016, and 2017. SFEI Contribution No. 840. San Francisco Estuary Institute: Richmond, CA.
2018. (5.55 MB)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. (2 MB)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. (146.43 KB)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. (636.35 KB)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. (2.37 MB)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. (2.25 MB)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. (2.83 MB)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. (4.26 MB)Prioritizing Candidate Green Infrastructure Sites within the City of Ukiah: A Demonstration of the Site Locator Tool of GreenPlan-IT. Report prepared for the City of Ukiah Department of Public Works under Supplemental Environmental Project # R1-018-0024. San Francisco Estuary Institute: Richmond. CA.
2019. (1.62 MB)This report describes the application of GreenPlan-IT’s Site Locator Tool to identify and rank candidate GI installation sites within the City of Ukiah. The Site Locator Tool is the first (foundational) tool of the GreenPlan-IT toolkit, meaning that the outputs are required inputs for both the Hydrologic Modeling and Optimization tools. The Site Locator Tool addresses the question: where are the best locations for GI implementation based on local planning priorities?
Priority margin unit stormwater monitoring to support load estimates of PCBs into San Leandro Bay and the Emeryville Crescent. SFEI Contribution No. 1088. San Francisco Estuary Institute: Richmond, CA.
2022. (2.06 MB)Procedures for the Collection and Storage of Environmental Samples in the RMP Specimen Bank. San Francisco Estuary Institute: Oakland, CA.
2010. (545.86 KB)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. Appendix C in:. . California Department of Fish and Game, Office of Oil Spill Prevention and Response, Sacramento CA.
2001. 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. (284.28 KB)Project: Statistical Design, Analysis and Guidance on the Pajaro and Lower Peninsula Watershed Assessments. TASK 3: GRTS Survey Designs and Sample Draws Memorandum – Pajaro and Lower Peninsula Watersheds. SFEI Contribution No. 763.
2015. (641.94 KB)A Proposed Lentic Benthic Bioassessment Procedure for California (Protocol Brief for Biological Sampling in Lakes, Reservoirs, and Ponds). SFEI Contribution No. 315. San Francisco Estuary Institute.
2004. (455.8 KB)Protocol for Accessing and Sampling Archived Sediments from the San Francisco Estuary RMP for Trace Substances. SFEI Contribution No. 119. San Francisco Estuary Institute.
. 2000. (197.08 KB) 2001.
The Pulse of the Bay 2019: Pollutant Pathways. SFEI Contribution No. 954. San Francisco Estuary Institute: Richmond, CA.
. 2019. (21.42 MB)The Pulse of the Bay: The 25th Anniversary of the RMP. SFEI Contribution No. 841. San Francisco Estuary Institute: Richmond, CA.
. 2017. (15.72 MB)The Pulse of the Delta: Linking Science & Management through Regional Monitoring. Aquatic Science Center: Richmond, CA.
. 2012. (17.41 MB)The Pulse of the Delta: Monitoring and Managing Water Quality in the Sacramento - San Joaquin Delta. Aquatic Science Center: Oakland, CA.
. 2011. (13.18 MB)The Pulse of the Estuary: Tracking Contamination with the Regional Monitoring Program 1993-1998. SFEI Contribution No. 100. San Francisco Estuary Institute.
2000. (4.21 MB)Pyrethroid Insecticides: An Analysis of Use Patterns, Distributions, Potential Toxicity and Fate in the Sacramento-San Joaquin Delta and Central Valley. SFEI Contribution No. 415. San Francisco Estuary Institute.
2005. (2.99 MB)QAPP for environmental monitoring and assessment program West Coast Pilot 2002 Intertidal Assessment: California Intensification. SFEI Contribution No. 234. San Francisco Estuary Institute: Oakland, CA.
2001. (489.07 KB)Quality Assurance in Environmental Analysis Applied to the San Francisco Estuary. SFEI Contribution No. 168. San Francisco Estuary Project: Oakland, CA.
1991. Quality Assurance Project Plan: Investigations of Sources and Effects of Pyrethroid Pesticides in Watersheds of the San Francisco Bay Estuary. San Francisco Estuary Institute: Oakland.
2007. (1.07 MB)Rapid Assessment Channel Survey for Exotic Species in San Francisco Bay - November 2005. SFEI Contribution No. 454. San Francisco Estuary Institute: Oakland, CA. p 7.
2005. (132.82 KB)Rapid Assessment Shore Survey for Exotic Species in San Francisco Bay - May 2004. SFEI Contribution No. 453. San Francisco Estuary Institute: Oakland, CA. p 32.
2005. (686.62 KB)A Rapid Assessment Survey of Exotic Species in Sheltered Coastal Waters. SFEI Contribution No. 508.
2002. A Rapid Assessment Survey of Nonindigenous Species in the Shallow Waters of Puget Sound. SFEI Contribution No. 223.
1998. (107.92 KB)Recalculating the Tule Factor. A report for The Bay Institute of San Francisco: Sausalito, CA.
1988. Recommendations for a Bioaccumulation Monitoring and Human Health Risk Reduction Program for California. SFEI Contribution No. 545.
2008. (3.03 MB)Recommendations for a Modeling Framework to Answer Nutrient Management Questions in the Sacramento-San Joaquin Delta. Central Valley Regional Water Quality Control Board: Rancho Cordova, CA.
2016. (542.21 KB)Recommendations for Improvement of RMP Sediment Monitoring. San Francisco Estuary Institute: Richmond, CA.
1999. (104.89 KB)Reconnecting Riverside with its River: Integrating Historical and Urban Ecology for a Healthier Future. SFEI Contribution No. 1133. San Francisco Estuary Institute: Richmond, Ca.
2023. (65.92 MB) (8.46 MB)Re-design Process of the San Francisco Estuary Regional Monitoring Program for Trace Substances (RMP) Status & Trends Monitoring Component for Water and Sediment. SFEI Contribution No. 507. San Francisco Estuary Institute: Oakland, CA.
2005. (1.72 MB)Re-design Process of the San Francisco Estuary Regional Monitoring Program for Trace Substances (RMP). SFEI Contribution No. 109. San Francisco Estuary Institute: Oakland, CA.
2004. (1.72 MB)Reducing Methylmercury Accumulation in the Food Webs of San Francisco Bay and Its Local Watersheds. SFEI Contribution No. 707. San Francisco Estuary Institute: Richmond, CA.
2014. (1.87 MB)Re-evaluation of the Floating Percentile Method for Deriving Dredged Sediment Screening Guidelines. SFEI Contribution No. 1143. San Francisco Estuary Institute: Richmond, California.
2023. (3.4 MB)This document summarizes a study conducted for the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) to re-evaluate the use of the Floating Percentile Method
(FPM) to derive sediment screening guidelines for dredged material reuse in the San Francisco Bay Region. The Long Term Management Strategy (LTMS) has a goal to use at least 40% of the sediment dredged from San Francisco Bay for beneficial reuse (USACE, 1998). The suitability of dredged sediment for beneficial reuse is in part determined by concentrations of toxic pollutants.The San Francisco Regional Water Quality Control Board (SFB-RWQCB) issued draft screening criteria in 2000 to categorize the suitability of sediment for reuse as either “surface” sediment, that may be placed near the surface for re-use in wetlands, or “foundation” sediment, that is buried under sediment that meets surface criteria. Contaminant concentration guidelines for surface sediment are lower than foundation sediment, based on the assumption that biota are more likely to be exposed to surface sediment than deeper foundation sediment.
Regional Analysis of Potential Beneficial Use Locations. Conducted for the San Francisco Bay Regional Dredged Material Management Plan. Prepared by the San Francisco Estuary Institute for the US Army Corps of Engineers, San Francisco District. SFEI Contribution No. 1178. San Francisco Estuary Institute: Richmond, CA.
2023. (12.17 MB)Regional Curves of Hydraulic Geometry for Wadeable Streams In Marin and Sonoma Counties, San Francisco Bay Area. Watershed Sciences Berkeley and Marin County Flood Control District.
2013. (2.85 MB)Regional Monitoring in San Francisco Bay: A Summary of Key Issues. SFEI Contribution No. 36.
1999. 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.
2005. (122.62 KB)The Regional Monitoring Program: Science in Support of Managing Water Quality in San Francisco Bay. SFEI Contribution No. 435.
2006. (239.75 KB)Regional Watershed Modeling and Trends Implementation Plan. SFEI Contribution No. 943. San Francisco Estuary Institute: Richmond, CA.
2019. (2.25 MB)Regional Watershed Spreadsheet Model (RWSM) Year 5 Progress Report. SFEI Contribution No. 788.
2016. (1.82 MB)Regional Watershed Spreadsheet Model (RWSM): Year 6 Progress Report. SFEI Contribution No. 811. San Francisco Estuary Institute: Richmond, CA.
2017. (1.79 MB) 2008.
The Relationship between Landscape Features and Sport Fish Mercury in the Sacramento-San Joaquin Delta Watershed. SFEI Contribution No. 534. San Francisco Estuary Institute.
2007. (22.59 MB)