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Recalculating the Tule Factor. A report for The Bay Institute of San Francisco: Sausalito, CA.
1988. A Rapid Assessment Survey of Nonindigenous Species in the Shallow Waters of Puget Sound. SFEI Contribution No. 223.
1998. (107.92 KB)A Rapid Assessment Survey of Exotic Species in Sheltered Coastal Waters. SFEI Contribution No. 508.
2002. 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)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)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)Quality Assurance in Environmental Analysis Applied to the San Francisco Estuary. SFEI Contribution No. 168. San Francisco Estuary Project: Oakland, CA.
1991. 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)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)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)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 Delta: Linking Science & Management through Regional Monitoring. Aquatic Science Center: Richmond, CA.
. 2012. (17.41 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 Bay 2019: Pollutant Pathways. SFEI Contribution No. 954. San Francisco Estuary Institute: Richmond, CA.
. 2019. (21.42 MB) 2001.
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)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)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)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 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: 2004 Rapid Assessment Survey for Exotic Species in San Francisco Bay. SFEI Contribution No. 451. San Francisco Estuary Institute: Oakland, Ca.
2005. Procedures for the Collection and Storage of Environmental Samples in the RMP Specimen Bank. San Francisco Estuary Institute: Oakland, CA.
2010. (545.86 KB)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)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?
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)Presence of marine invasive species along the coast of Massachusetts. SFEI Contribution No. 509.
2002. Preliminary Simulations of Sediment Dynamics in the South San Francisco Bay. San Francisco Estuary Institute: Oakland, CA.
2011. (2.83 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. Power Analysis and Optimization of the RMP Status and Trends Program. SFEI Contribution No. 555.
2008. (2.25 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. 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)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)The Potential Distribution and Abundance of Zebra Mussels in California. SFEI Contribution No. 225. San Francisco Estuary Institute: Richmond, CA.
1998. (146.43 KB)Potential biological indicators of contaminant effects for use in monitoring the San Francisco Estuary. SFEI Contribution No. 43. San Francisco Estuary Institute.
2001. Polychlorinated Biphenyls in Northern San Francisco Estuary Refinery Effluents. SFEI Contribution No. 510.
2002. 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)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)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 2015-2018. SFEI Contribution No. 942. San Francisco Estuary Institute: Richmond, CA.
2019. (3.37 MB)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 final progress report, water years 2015 and 2016. SFEI Contribution No. 817.
2017. (4.01 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 (POC) loads monitoring progress report, water years (WYs) 2012, 2013, and 2014. SFEI Contribution No. 741.
2016. (2.58 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 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 progress report, water year (WY) 2012. SFEI: Richmond, CA.
2013. (2.33 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)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)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 Sediment Source Assessment: Pavon Creeks Sub-basin. SFEI Contribution No. 515. San Francisco Estuary Institute. p 67.
2006. (51.71 MB) (25.63 MB)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)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)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)Phase 2 (2003) Bioassessment of Waterbodies Treated with Aquatic Pesticides. SFEI Contribution No. 117. San Francisco Estuary Insitute: Oakland, CA.
2004. (577.14 KB)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. 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.
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.
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 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 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)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)Peninsula Watershed Historical Ecology Study. SFEI Contribution No. 1029. San Francisco Estuary Institute: Richmond, Ca.
2021. (204.95 MB) (21.97 MB)Pelagic Organism Decline. SFEI Contribution No. 511.
2005. 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.
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 effluent. SFEI Contribution No. 237.
2001. PCB intercalibration exercise with Regional Monitoring Program water sample extracts. SFEI Contribution No. 204. San Francisco Estuary Institute: Richmond, CA. pp 234-239.
1997. A PCB Budget for San Francisco Bay. SFEI Contribution No. 376. San Francisco Estuary Institute: Oakland, CA.
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. (421.66 KB)Pathogen Occurrence and Analysis in Relation to Water Quality Attainment in San Francisco Bay Area Watersheds. SFEI Contribution No. 128.
2002. (133.07 KB) 1998.
1999.
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. (194.22 KB)Organochlorine Pesticide Fate in San Francisco Bay. SFEI Contribution No. 433. San Francisco Estuary Institute: Oakland, CA. p 48.
2006. (1.93 MB)Optimizing Transplanted Bivalve Studies for the Regional Monitorig Program for Trace Substances. . SFEI Contribution No. 431. San Francisco Estuary Institute.
2005. (1.25 MB)Optimizing sampling methods for pollutant loads and trends in San Francsico Bay urban stormwater monitoring. San Francisco Estuary Institute: Oakland, CA.
2010. (1.6 MB)Online 401: From Pilot to Production. San Francisco Estuary Institute: Richmond, CA.
2014. (3.15 MB)Ohio Rapid Assessment Method for Wetlands v. 5.0 Users Manual and Scoring Forms. State of Ohio Environmental Protection Agency: Ohio. p 107.
. 2001. Observations on trace organic concentrations in RMP water samples. SFEI Contribution No. 210. San Francisco Estuary Institute. pp 67-77.
1997. Observational Study of Sycamore Regeneration at two sites in Santa Clara County after the 2016-2017 Water Year. SFEI Contribution No. 874.
2018. (8.44 MB)Nutrient Stormwater Monitoring Results: WY2012 and WY2013. San Francisco Estuary Institute: Richmond, CA.
2014. (2.27 MB)Nutrient Moored Sensor Program: Year 1 Progress Update. SFEI: Richmond, CA.
2014. (6.61 MB)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 Management Strategy Science Program. SFEI Contribution No. 879. San Francisco Estuary Institute: Richmond, CA.
2017. (49.7 MB)Nutrient Management Strategy Science Plan Report. SFEI Contribution No. 878. San Francisco Estuary Institute: Richmond, CA.
2016. (9.78 MB)Novato Creek Baylands Vision: Integrating ecological functions and flood protection within a climate-resilient landscape. SFEI Contribution No. 764.
2015. (21.5 MB)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.
Novato Creek Baylands Historical Ecology Study. SFEI Contribution No. 740. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.
2015. (27.13 MB)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.
Northern San Diego County Lagoons Historical Ecology Investigation. SFEI Contribution No. 722. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 215.
2014. (305.02 MB) (50.9 MB)North Bay Selenium Monitoring Design. SFEI Contribution No. 921. San Francisco Estuary Institute : Richmond, CA.
2018. (2.08 MB)2023. North Bay Selenium 2019-20 QA Summaries. San Francisco Estuary Institute: Richmond, CA.
(108.07 KB)North Bay Mercury Biosentinel Project (December 2014 Report). SFEI Contribution No. 738. San Francisco Estuary Institute: Richmond, CA.
2014. (2.88 MB)