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SFEI. 2006. The 2004 to 2005 RMP Annual Monitoring Results. Regional Monitoring Program for Water Quality in the San Francisco Estuary (RMP). SFEI Contribution No. 519. San Francisco Estuary Institute. p 220.
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SFEI. 2016. 2016 RMP Sturgeon Derby Study Sampling & Analysis Plan. San Francisco Estuary Institute : Richmond, CA.
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SFEI. 2015. 2015 Sturgeon Muscle Plug Study Sampling & Analysis Plan. San Francisco Estuary Institute : Richmond, CA.
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SFEI. 2012. 2011 Pulse of the Estuary: Pollutant Effects on Aquatic Life. SFEI Contribution No. 660. San Francisco Estuary Institute : Richmond, CA. p 104.
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SFEI. 2015. 2015 Pulse of the Bay: The State of Bay Water Quality - 2015 and 2065. SFEI Contribution No. 759. San Francisco Estuary Institute: Richmond, CA.
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SFEI. 2013. 2013 Pulse of the Bay: Contaminants of Emerging Concern. San Francisco Estuary Institute : Richmond, CA. p 102.
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SFEI. 2009. 2009 Pulse of the Estuary: Bay Sediments - Past a Tipping Point. SFEI Contribution No. 583. San Francisco Estuary Institute: Oakland, CA. p 92.
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SFEI. 2008. 2008 Pulse of the Estuary: Monitoring and Managing Water Quality in the San Francisco Estuary. SFEI Contribution No. 559. San Francisco Estuary Institute: Oakland, CA.
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SFEI. 2007. 2007 Pulse of the Estuary: Monitoring and Managing Water Quality in the San Francisco Estuary. SFEI Contribution No. 532. San Francisco Estuary Institute: Oakland, CA. p 88.
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SFEI. 2005. 2005 Pulse of the Estuary: Monitoring and Managing Water Quality in the San Francisco Estuary. SFEI Contribution No. 78. San Francisco Estuary Institute: Oakland, CA. p 84.
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SFEI. 2004. 2004 Pulse of the Estuary: Monitoring & Managing Contamination in the San Francisco Estuary. SFEI Contribution No. 401. San Francisco Estuary Institute : Oakland, CA.
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SFEI. 2001. 1993 - 1999 Pulse of the Estuary: Monitoring and Managing Contamination in the San Francisco Estuary. SFEI Contribution No. 101. San Francisco Estuary Institute: Oakland, CA.
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SFEI. 2003. 2003 Pulse of the Estuary: Monitoring & Managing Contamination in the San Francisco Estuary. SFEI Contribution No. 74. San Francisco Estuary Institute : Oakland, CA.
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SFEI; CDHS,. 2001. The San Francisco Bay Seafood Consumption Study Report. SFEI Contribution No. 369. San Francisco Estuary Institute: Oakland, CA.
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SFEI; Safran, S. M. 2014. Natural Flow Hydrodynamic Modeling Technology Support Phase 1 Technical Memorandum.

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.

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SFEI. 2010. 2010 Pulse of the Estuary: Linking the Watersheds and the Bay. SFEI Contribution No. 618. San Francisco Estuary Institute : Oakland, CA. p 96.
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Senn, D. B.; Novick, E. 2014. Suisun Bay Ammonium Synthesis. SFEI Contribution No. 706. San Francisco Estuary Institute: Richmond, CA. p 191.
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Senn, D.; Novick, E. 2016. Nutrient Management Strategy Science Plan Report. SFEI Contribution No. 878. San Francisco Estuary Institute: Richmond, CA.
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Senn, D.; Trowbridge, P. 2016. San Francisco Bay Nutrient Management Strategy Observation Program. SFEI Contribution No. 877. San Francisco Estuary Institute: Richmond, CA.
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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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RMP Lead Scientist. 2015. 2015 RMP Artesian Slough Sampling & Analysis Plan. San Francisco Estuary Institute: Richmond, CA.
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Applied Marine Sciences. 2015. 2015 RMP Water Cruise Report. Applied Marine Sciences: Livermore, CA.
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Applied Marine Sciences. 2015. 2015 RMP Water Cruise Plan. Applied Marine Sciences: Livermore, CA.
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Applied Marine Sciences. 2014. 2013 RMP Water Cruise Plan. Applied Marine Sciences: Livermore, CA.
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Schoellhamer, D.; McKee, L.; Pearce, S.; Kauhanen, P.; Salomon, M.; Dusterhoff, S.; Grenier, L.; Marineau, M.; Trowbridge, P. 2018. Sediment Supply to San Francisco Bay. SFEI Contribution No. 842. San Francisco Estuary Institute : Richmond, CA.
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Schoellhamer, D. H. 1996. Factors affecting suspended-solids concentrations in South San Francisco Bay, California. Journal of Geophysical Research 101, 12,087-12,095 . SFEI Contribution No. 10.
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Schiff, K.; Trowbridge, P. R.; Sherwood, E. T.; Tango, P.; Batiuk, R. A. 2016. Regional monitoring programs in the United States: Synthesis of four case studies from Pacific, Atlantic, and Gulf Coasts. Regional Studies in Marine Science 4.

Water quality monitoring is a cornerstone of environmental protection and ambient monitoring provides managers with the critical data they need to take informed action. Unlike site-specific monitoring that is at the heart of regulatory permit compliance, regional monitoring can provide an integrated, holistic view of the environment, allowing managers to obtain a more complete picture of natural variability and cumulative impacts, and more effectively prioritize management actions. By reviewing four long-standing regional monitoring programs that cover portions of all three coasts in the United States–Chesapeake Bay, Tampa Bay, Southern California Bight, and San Francisco Bay–important insights can be gleaned about the benefits that regional monitoring provides to managers. These insights include the underlying reasons that make regional monitoring programs successful, the challenges to maintain relevance and viability in the face of ever-changing technology, competing demands and shifting management priorities. The lessons learned can help other managers achieve similar successes as they seek to establish and reinvigorate their own monitoring programs.

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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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Salop, P. 2017. 2017 RMP Water Cruise Report. SFEI Contribution No. 846. Applied Marine Sciences: Livermore, CA.
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Salop, P.; Franz, A. 2018. 2018 RMP Sediment Cruise Report. SFEI Contribution No. 907. San Francisco Estuary Institute : Richmond, CA.
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Salop, P.; Gunther, A. J.; Bell, D.; Cotsifas, J.; Gold, J.; Ogle, S. R. 2001. San Francisco Bay Episodic Toxicity Report - 2000. SFEI Contribution No. 233. San Francisco Estuary Institute: Richmond, CA.
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Salop, P.; Bell, D.; Gold, J. 1999. Field Sampling Manual for the RMP for Trace Substances (version 1, January 1999). SFEI Contribution No. 324. San Francisco Estuary Institute: Richmond, CA.
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Salop, P. 2018. 2018 RMP Bivalve Deployment Cruise Report. SFEI Contribution No. 903. San Francisco Estuary Institute : Richmond, CA.
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Salop, P.; Gunther, A.; Bell, D.; Cotsifas, J.; Gold, J.; Ogle, S. 2002. Episodic Ambient Water Toxicity in the San Francisco Estuary. SFEI Contribution No. 51. San Francisco Estuary Institute: Oakland, CA.
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Salomon, M.; Dusterhoff, S. D.; Askevold, R. A.; Grossinger, R. M. 2016. San Francisquito Creek Baylands: Landscape Change Metrics Analysis. Flood Control 2.0. SFEI Contribution No. 784. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 12.

Major Findings
Over the past 150 years, lower San Francisquito Creek and the adjacent baylands have been modified for the sake of land reclamation and flood control. This study focused on developing an understanding of the magnitude of habitat change since the mid-19th century through comparisons of key historical and contemporary landscape-scale habitat features, as well as several key landscape metrics that relate to ecological functions and landscape resilience. The major findings from the analyses conducted for this study are as follows:
• Historically, the San Francisquito Creek Baylands included a mosaic of habitat types, including an extensive tidal marsh plain with salt pannes and an expansive tidal channel network, a broad bay flat, and a relatively wide contiguous low-gradient tidal-terrestrial transition zone.
• Since the late 19th century, a combination of land reclamation and the inland migration of the shoreline has resulted in a 55% decrease in tidal marsh area, a 67% decrease in total tidal channel length, a 40% reduction in channel flat area, a 20% increase in bay flat area, and a 95% decrease in tidal-terrestrial transition zone length.
• Land reclamation has also resulted in the creation of new features that did not exist in the area historically including tidal lagoons, non-tidal open water features, and non-tidal wetlands.
 

Recommendations
The findings from this study provide insight into the drivers for and magnitude of habitat change within the San Francisquito Creek Baylands, and can therefore help inform climate-resilient approaches for regaining some of the lost landscape features and ecological functions. Specific management recommendations developed from the study findings are as follows:
• The dramatic decrease in tidal marsh area and associated tidal channel length since the mid-1800s make tidal marsh restoration a high priority. To make restored areas sustainable over the long-term, restoration should include reestablishing regular tidal inundation as well as reestablishing a connection with San Francisquito Creek and the delivery of freshwater and fine sediment. Restoration efforts should focus on large contiguous areas with minimal infrastructure and should ideally be done sometime over the next decade to ensure the restored areas will have a chance of surviving the sharp increase in the rate of sea level rise that is predicted to occur around 2030 (Goals Update 2015).
• Similarly, the dramatic decrease in the tidal-terrestrial transition zone makes it a high priority for any restoration vision for this area. The transition zone provides distinct ecological services and marsh migration space, and is in need of restoration throughout the South Bay. Since most of the upland land along the historical tidal-terrestrial transition zone is currently developed, near-term restoration efforts should focus on creating transition zone habitats on the bayside of flood risk management levees (Goals Update 2015).
• The landscape metrics used in this study (tidal habitat area, tidal channel length, and tidal-terrestrial interface length) can be used to help design resilient landscape restoration and adaptation strategies around the mouth of San Francisquito Creek. Specifically, the metrics can be used to assess the long-term ecological benefit associated with various processes-based restoration approaches (i.e., approaches that create habitat features and establish physical processes required for habitat resilience). Additional useful landscape metrics are being developed as part of the Resilient Silicon Valley project (see Robinson et al. 2015).

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Salomon, M.; Baumgarten, S.; Dusterhoff, S. D.; Beller, E. E.; Askevold, R. A. 2015. Novato Creek Baylands Historical Ecology Study. SFEI Contribution No. 740. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.

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.

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Salomon, M.; San Francisco Estuary Institute; Costa, Cof Contra. 2011. Contra Costa County 1939 Aerial Photomosaic, GIS layer containing orthorectified historical aerial imagery of Contra Costa County from 1939.
Safran, S. M. 2015. The Tijuana River Valley: An Ecological Look into the Past.

Hot springs in the Tijuana River? Antelope by the beach? Zip-lines over the international border?
Come find out what the Tijuana River Valley looked like in the not-so-distant past and how the river, estuary, and surrounding areas have changed over the past two centuries. Hear how researchers “recreated” the historical landscape and how this information helps us to better plan for the future.

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Safran, S. M.; Baumgarten, S. A.; Beller, E. E.; Crooks, J. A.; Grossinger, R. M.; Lorda, J.; Longcore, T. R.; Bram, D. L.; Dark, S. J.; Stein, E. D.; et al. 2017. Tijuana River Valley Historical Ecology Investigation. Prepared for the State Coastal Conservancy. A Report of SFEI-ASC’s Resilient Landscapes Program. SFEI Contribution No. 760. San Francisco Estuary Institute - Aquatic Science Center : Richmond, CA. p 230.

The Tijuana River Valley Historical Ecology Investigation addresses a regional data gap by reconstructing the landscape and ecosystem characteristics of the river valley prior to the major modifications of the late 19th and 20th centuries. The research presented here, funded by the California State Coastal Conservancy, supplies foundational information at the regional and system scale about how the Tijuana Estuary, River, and valley looked and functioned in the recent past, as well as how they have changed over time. The ultimate goal of this study is to provide a new tool and framework that, in combination with contemporary research and future projections, can support and guide ongoing restoration design, planning, and management efforts in the valley.

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Safran, S. M.; Baumgarten, S. A.; Beller, E. E.; Bram, D. L.; Crooks, J. A.; Dark, S. J.; Grossinger, R. M.; Longcore, T. R.; Lorda, J.; Stein, E. D. 2018. The Historical Ecology of the Tijuana Estuary & River Valley (Restore America's Estuaries 2018 Conference Presentation).

This talk was given at the 2018 Restore America's Estuary Conference in Long Beach, CA as part of a special session titled "Restoration Perspectives from the Tijuana River National Estuarine Research Reserve." It is based on information from the Tijuana River Valley Historical Ecology Investigation, a report published in 2017.


Though many areas of the binational Tijuana River watershed remain relatively undeveloped, land and water use changes over the past 200 years have resulted in significant ecological impacts, particularly in the more urbanized areas of the lower watershed. Drawing upon a diverse set of historical data, we reconstructed the ecological and hydrogeomorphic conditions of the lower Tijuana River valley prior to major Euro-American modification (ca. 1850) and documented major changes in habitat distribution and physical processes over this time. The river corridor, which was historically dominated by riparian scrub, today instead supports dense stands of riparian forest. The valley bottom surrounding the river corridor, which historically supported extensive seasonal wetlands, has largely been converted to drier habitat types and agricultural uses. The estuary, which historically supported large expanses of salt marsh and mudflat as well as seasonally dry salt flats, has retained much of its former extent and character, but has been altered by increased sediment input and other factors. The new information about the historical landscape presented here is relevant to a number of issues scientists and managers are dealing with today, including the conservation of endangered species, the fate of the valley’s riparian habitats after the recent invasion of invasive shot-hole borer beetles, and the effects on groundwater levels on native plant communities. We will also draw from other historical ecology studies conducted in Southern California to illustrate how the information about the past has been utilized to improve the functioning and resilience of nearby coastal ecosystems.

Presentation recording: available here.

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Safran, S. M.; Clark, E.; Beller, E. E.; Grossinger, R. M. 2016. Mission Bay Historical Ecology Reconnaissance Study: Data Collection Summary (Technical Report). SFEI Contribution No. 777.

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.

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Safran, S. M.; Grenier, J. Letitia; Grossinger, R. M. 2016. Ecological implications of modeled hydrodynamic changes in the upper San Francisco Estuary: Phase II Technical Memorandum. SFEI Contribution No. 786.

The physical and ecological environment of the upper San Francisco Estuary has been profoundly altered since the early 1800s. Recent efforts have utilized maps of the upper estuary’s historical habitat types to infer associated changes in desired ecosystem processes and functions. The work presented in this memo builds on these previous efforts, but utilizes a new tool for evaluating change over time: a 3D hydrodynamic model of the pre-development estuary. This model was constructed by Resource Management Associates (RMA) using a new digital elevation model of the pre-development upper estuary generated by SFEI and UC Davis (UCD) and “natural” boundary flows calculated by the California Department of Water Resources (CDWR).


Once completed and calibrated, the pre-development model was paired with a similar model of the contemporary system in order to analyze hydrodynamic changes in the upper estuary. These analyses are presented in a technical memorandum published by RMA (2015). This memorandum takes these analyses and considers the ecological implications of modeled changes (see the “Results” section). Hydrodynamic analyses include analyzing changes in tidal prism, isohaline positions, low-salinity zone habitat, channel velocity, and source water distribution.


 In addition to describing the ecological implications of modeled hydrodynamic changes, this memorandum summarizes major ongoing questions about estuarine hydrodynamics that might be explored using these models, including changes in water residence time, temperature, transport pathways, and the connectivity of aquatic and semi-aquatic habitats. Understanding changes in these and other factors would greatly improve our understanding of the desirable ecosystem functions provided by the historical system and, as a result, improve our ability to recover these functions now and into the future.

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Safran, S. M.; Hagerty, S.; Robinson, A.; Grenier, L. 2018. Translating Science-Based Restoration Strategies into Spatially-Explicit Restoration Opportunities in the Delta (2018 Bay-Delta Science Conference Presentation).

In a previous report titled “A Delta Renewed” we offered a collection of guidelines for science-based ecological restoration in the Sacramento-San Joaquin Delta that emphasized restoring or emulating natural processes, anticipating future changes associated with climate change, establishing appropriate configurations of habitat types at the landscape scale, and utilizing a variety multi-benefit management strategies. In this talk, we present on our recent work to support regional restoration planning efforts by developing a repeatable process for using these guidelines to identify spatially-explicit restoration opportunities. The process is largely GIS-based and utilizes spatial data on existing land cover and conservation status, habitat configuration (including patch sizes and distances), surface elevations (including depth of subsidence), and future changes in tidal elevations associated with sea-level rise.  By distilling generalized guidelines into spatially-explicit opportunities, we hope to provide a practical tool for incorporating science into planning. To that end, these new methods are currently being piloted through planning efforts focused on the Central Delta Corridor and the McCormack Williamson Tract, and are also being used to assist with the quantification of ecological restoration potential in the Delta Plan Ecosystem Amendment.

Presentation recording: available here.

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Sadaria, A. M.; Sutton, R.; Moran, K. D.; Teerlink, J.; Brown, J. V.; Halden, R. U. 2017. Passage of fiproles and imidacloprid from urban pest control uses through wastewater treatment plants in northern California. Environmental Toxicology and Chemistry 36, 1473-1482 . SFEI Contribution No. 783.

Urban pest control insecticides, specifically fipronil and its four major degradates (fipronil sulfone, sulfide, desulfinyl, and amide) and imidacloprid, were monitored during drought conditions in eight San Francisco Bay wastewater treatment plants (WWTPs). In influent and effluent, ubiquitous detections were obtained in units of ng/L for fipronil (13-88), fipronil sulfone (1-28), fipronil sulfide (1-5) and imidacloprid (58-306). In influent, 100% of imidacloprid and 62 ± 9% of total fiproles (fipronil and degradates) were present in the dissolved state, with the balance being bound to filter-removable particulates. Targeted insecticides persisted during wastewater treatment, regardless of treatment technology utilized (imidacloprid: 93 ± 17%; total fiproles: 65 ± 11%), with partitioning into sludge (3.7-151.1 μg/kg dry weight as fipronil) accounting for minor losses of total fiproles entering WWTPs. The load of total fiproles was fairly consistent across the facilities but fiprole speciation varied. This first regional study on fiprole and imidacloprid occurrences in raw and treated California sewage revealed ubiquity and marked persistence to conventional treatment of both phenylpyrazole and neonicotinoid compounds. Flea and tick control agents for pets are identified as potential sources of pesticides in sewage meriting further investigation and inclusion in chemical-specific risk assessments. 

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Ruhl, C. A.; Schoellhamer, D. H. 1998. Technical Report of the San Francisco Estuary Regional Monitoring Program for Trace Substances. SFEI Contribution No. 375. San Francisco Estuary Institute: Richmond, CA.
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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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