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Davis, J.; Buzby, N. 2021. PCBs in Shiner Surfperch in Priority Margin Areas of San Francisco Bay. SFEI Contribution No. 1054.

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. 

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Oros, D. R. 2005. Pelagic Organism Decline. SFEI Contribution No. 511.
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Sedlak, M.; Sutton, R.; Wong, A.; Lin, D. 2018. Per and Polyfluoroalkyl Substances (PFAS) in San Francisco Bay: Synthesis and Strategy. SFEI Contribution No. 867. San Francisco Estuary Institute : Richmond, CA.
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Sedlak, M.; Greig, D. 2012. Perfluoroalkyl compounds (PFCs) in wildlife from an urban estuary. Journal of Environmental Monitoring 14, 146-154.
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Sonoma Land Trust and partners. 2023. 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.
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Peterson, D.; Baumgarten, S.; Stark, K.; Vaughn, L.; Dusterhoff, S. 2024. Petaluma River Watershed Contemporary Riparian Condition Assessment. Petaluma River Watershed Contemporary Riparian Condition Assessment. SFEI Contribution No. 1160. San Francisco Estuary Institute: Richmond, CA.
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Baumgarten, S.; Clark, E.; Dusterhoff, S.; Grossinger, R. M.; Askevold, R. A. 2018. Petaluma Valley Historical Hydrology and Ecology Study. SFEI Contribution No. 861. San Francisco Estuary Institute: Richmond, CA.

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.

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Mendez, M.; Trinh, M.; Miller, E.; Lin, D.; Sutton, R. 2022. PFAS in San Francisco Bay Water. SFEI Contribution No. 1094. San Francisco Estuary Institute: Richmond, CA.

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.

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Vuckovic, D.; MacDonald, J. A.; Lin, D.; Méndez, M.; Miller, E.; Mitch, W. 2023. Pharmaceuticals, pesticides, and ultraviolet filters in wastewater discharges to San Francisco Bay as drivers of ecotoxicity. Environmental Pollution 336 . SFEI Contribution No. 1153.

Research in the United States evaluating ecotoxic risk to receiving waters posed by contaminants occurring in wastewater discharges typically has focused on measurements of pharmaceuticals and personal care products (PPCPs), with limited evaluations of UV filters and phenylpyrazole and neonicotinoid pesticides. In this study, concentrations of 5 representative pharmaceuticals, 11 pesticides or pesticide degradation products, and 5 ultraviolet filters were measured in 24 h composite samples of six wastewater discharges representing ∼70% of the total wastewater discharged to San Francisco Bay during the summer and fall of 2021. No significant difference was observed between concentrations measured on weekdays vs. weekends. A hydrodynamic model of San Francisco Bay was used to estimate annual average dilution factors associated with different subembayments. With and without considering dilution effects, Risk Quotients were calculated using the 90th percentile of measured concentrations in wastewater effluents and threshold concentrations associated with ecotoxicity. Risk Quotients were highest for the neonicotinoid pesticide, imidacloprid, and exceeded ecotoxicity thresholds in the lower South Bay by a factor of 2.4, even when considering dilution. Compared to commonly measured pharmaceuticals, Risk Quotients for imidacloprid were higher than those for carbamazepine, trimethoprim and diclofenac, and comparable to those for propranolol and metoprolol. Risk Quotients for the pesticide, fipronil, and the UV filter, oxybenzone, were higher than for carbamazepine. The results highlight the need to incorporate pesticides and UV filters with high Risk Quotients into studies in the United States evaluating ecotoxic risk associated with contaminants in municipal wastewater discharges.

David, N.; Shonkoff, S. B.; Hayworth, J. 2004. Phase 2 (2003) Bioassessment of Waterbodies Treated with Aquatic Pesticides. SFEI Contribution No. 117. San Francisco Estuary Insitute: Oakland, CA.
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Jabusch, T. W.; Tjeerdema, R. S. 2006. Photodegradation of penoxsulam. Journal of Agricultural and Food Chemistry 54, 5958-5961.
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Flegal, A. R.; Bruland, K. W.; Sanudo-Wilhelmy, S. A.; Kozelka, P. B. 1997. Physicochemical speciation of lead in South San Francisco Bay. Estuarine, Coastal and Shelf Science 44, 649-658 . SFEI Contribution No. 26.
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McKee, L. J. .; Pearce, S.; Shonkoff, S. 2006. Pinole Creek Sediment Source Assessment: Pavon Creeks Sub-basin. SFEI Contribution No. 515. San Francisco Estuary Institute. p 67.
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Cohen, A. N. 1995. Place Invaders. Energy and Resources News 4, 1-3.
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Cohen, A. N. 1993. Place Invaders. Pacific Discovery (Calif. Acad. Sci.) 46, 22-26.
Oros, D. R. 2002. Polar aromatic biomarkers in the miocene Maritza-East Lignite, Bulgaria. Organic Geo-chemistry . SFEI Contribution No. 476.
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Gilbreath, A.; Hunt, J.; Mckee, L. 2020. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015 - 2019. SFEI Contribution No. 987. San Francisco Estuary Institute: Richmond, CA.

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.

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Gilbreath, A.; Hunt, J.; Mckee, L. 2019. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2018. SFEI Contribution No. 942. San Francisco Estuary Institute: Richmond, CA.
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Gilbreath, A.; McKee, L.; Hunt, J. 2021. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2020. SFEI Contribution No. 1061. San Francisco Estuary Institute: Richmond, CA.

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.

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Gilbreath, A.; Wu, J.; Hunt, J.; McKee, L. 2018. Pollutants of Concern Reconnaissance Monitoring Water Years 2015, 2016, and 2017. SFEI Contribution No. 840. San Francisco Estuary Institute: Richmond, CA.
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Houtz, E. F.; Sutton, R.; Park, J. - S.; Sedlak, M. 2016. Poly- and perfluoroalkyl substances in wastewater: Significance of unknown precursors, manufacturing shifts, and likely AFFF impacts. Water Research . SFEI Contribution No. 780.

In late 2014, wastewater effluent samples were collected from eight treatment plants that discharge to San Francisco (SF) Bay in order to assess poly- and perfluoroalkyl substances (PFASs) currently released from municipal and industrial sources. In addition to direct measurement of twenty specific PFAS analytes, the total concentration of perfluoroalkyl acid (PFAA) precursors was also indirectly measured by adapting a previously developed oxidation assay. Effluent from six municipal treatment plants contained similar amounts of total PFASs, with highest median concentrations of PFHxA (24 ng/L), followed by PFOA (23 ng/L), PFBA (19 ng/L), and PFOS (15 ng/L). Compared to SF Bay municipal wastewater samples collected in 2009, the short chain perfluorinated carboxylates PFBA and PFHxA rose significantly in concentration. Effluent samples from two treatment plants contained much higher levels of PFASs: over two samplings, wastewater from one municipal plant contained an average of 420 ng/L PFOS and wastewater from an airport industrial treatment plant contained 560 ng/L PFOS, 390 ng/L 6:2 FtS, 570 ng/L PFPeA, and 500 ng/L PFHxA. The elevated levels observed in effluent samples from these two plants are likely related to aqueous film forming foam (AFFF) sources impacting their influent; PFASs attributable to both current use and discontinued AFFF formulations were observed. Indirectly measured PFAA precursor compounds accounted for 33%–63% of the total molar concentration of PFASs across all effluent samples and the PFAA precursors indicated by the oxidation assay were predominately short-chained. PFAS levels in SF Bay effluent samples reflect the manufacturing shifts towards shorter chained PFASs while also demonstrating significant impacts from localized usage of AFFF.

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Sutton, R.; Sedlak, M.; Davis, J. A. 2014. 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.
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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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Ross, J. R. M.; Oros, D. R. 2004. Polycyclic aromatic hydrocarbons in San Francisco Estuary sediments. Marine Chemistry 86, 169-184 . SFEI Contribution No. 82.
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Cohen, A. N.; Weinstein, A. 1998. The potential distribution and abundance of the zebra mussel in California. Eighth International Zebra Mussel and Aquatic Nuisance Species Conference, 65.
Weinstein, A.; Cohen, A. N. 1998. The potential distribution and abundance of zebra mussels in California. Dreissena! (New York Sea Grant) 9, 1-3 . SFEI Contribution No. 323.
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Cohen, A. N.; Weinstein, A. 1998. The Potential Distribution and Abundance of Zebra Mussels in California. SFEI Contribution No. 225. San Francisco Estuary Institute: Richmond, CA.
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Cohen, A. N.; Weinstein, A. 2001. 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.
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Greenfield, B. K.; Hrabik, T. R.; Harvey, C. J.; Carpenter, S. R. 2000. Predicting mercury levels in fish: use of water chemistry, trophic ecology, and spatial traits. Canadian Journal of Fisheries and Aquatic Sciences 58, 1419 -1429 . SFEI Contribution No. 306.
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Cohen, A. N. 1999. Prevention vs. control of biological invasions. First National Conference on Marine Bioinvasions.
Cloern, J. E.; Robinson, A.; Richey, A.; Grenier, J. Letitia; Grossinger, R. M.; Boyer, K. E.; Burau, J.; Canuel, E.; DeGeorge, J. F.; Drexler, J. Z.; et al. 2016. Primary Production in the Delta: Then and Now. San Francisco Estuary and Watershed Science 14 (3).

To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function. Primary production is a crucial ecosystem process, which directly limits the quality and quantity of food available for secondary consumers such as invertebrates and fish. The Delta has a low rate of primary production, but it is unclear whether this was always the case. Recent analyses from the Historical Ecology Team and Delta Landscapes Project provide quantitative comparisons of the areal extent of 14 habitat types in the modern Delta versus the historical Delta (pre-1850). Here we describe an approach for using these metrics of land use change to: (1) produce the first quantitative estimates of how Delta primary production and the relative contributions from five different producer groups have been altered by large-scale drainage and conversion to agriculture; (2) convert these production estimates into a common currency so the contributions of each producer group reflect their food quality and efficiency of transfer to consumers; and (3) use simple models to discover how tidal exchange between marshes and open water influences primary production and its consumption. Application of this approach could inform Delta management in two ways. First, it would provide a quantitative estimate of how large-scale conversion to agriculture has altered the Delta's capacity to produce food for native biota. Second, it would provide restoration practitioners with a new approach—based on ecosystem function—to evaluate the success of restoration projects and gauge the trajectory of ecological recovery in the Delta region.

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Lowe, S.; Kauhanen, P. 2019. 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.

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? 

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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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