Our library features many hundreds of entries.

To search among them, click "Search" below to pull down options, including filtering by document type, author, year, and keyword.
Find these options under "Show only items where." Or you can also sort by author, title, type, and year clicking the headings below.

Export 1654 results:
2019
Foley, M. 2019. 2019 Bay RMP Multi-Year Plan. SFEI Contribution No. 940. San Francisco Estuary Institute: Richmond, CA.
 (3.16 MB)
 (2.45 MB) (119.95 KB) (44.53 KB) (23.92 KB)
Sutton, R.; Chen, D.; Sun, J.; Greig, D. J.; Wu, Y. 2019. Characterization of brominated, chlorinated, and phosphate flame retardants in San Francisco Bay, an urban estuary. Science of the Total Environment 652, 212-223 . SFEI Contribution No. 859.

Flame retardant chemical additives are incorporated into consumer goods to meet flammability standards, and many have been detected in environmental matrices. A uniquely wide-ranging characterization of flame retardants was conducted, including polybrominated diphenyl ethers (PBDEs) and 52 additional brominated, chlorinated, or phosphate analytes, in water, sediment, bivalves, and harbor seal blubber of San Francisco Bay, a highly urbanized estuary once considered a hot spot for PBDE contamination. Among brominated flame retardants, PBDEs remained the dominant contaminants in all matrices, though declines have been observed over the last decade following their phase-out. Hexabromocyclododecane (HBCD) and other hydrophobic, brominated flame retardants were commonly detected at lower levels than PBDEs in sediment and tissue matrices. Dechlorane Plus (DP) and related chlorinated compounds were also detected at lower levels or not at all across all matrices. In contrast, phosphate flame retardants were widely detected in Bay water samples, with highest median concentrations in the order TCPP > TPhP > TBEP > TDCPP > TCEP. Concentrations in Bay water were often higher than in other estuarine and marine environments. Phosphate flame retardants were also widely detected in sediment, in the order TEHP > TCrP > TPhP > TDCPP > TBEP. Several were present in bivalves, with levels of TDCPP comparable to PBDEs. Only four phosphate flame retardants were detected in harbor seal blubber: TCPP, TDCPP, TCEP, and TPhP. Periodic, multi-matrix screening is recommended to track contaminant trends impacted by changes to flammability standards and manufacturing practices, with a particular focus on contaminants like TDCPP and TPhP that were found at levels comparable to thresholds for aquatic toxicity.

Yee, D.; Wong, A. 2019. Evaluation of PCB Concentrations, Masses, and Movement from Dredged Areas in San Francisco Bay. SFEI Contribution No. 938. San Francisco Estuary Institute: Richmond, CA.
 (876.18 KB)
Gilbreath, A.; McKee, L.; Shimabuku, I.; Lin, D.; Werbowski, L. M.; Zhu, X.; Grbic, J.; Rochman, C. 2019. Multi-year water quality performance and mass accumulation of PCBs, mercury, methylmercury, copper and microplastics in a bioretention rain garden. SFEI Contribution No. 872. San Francisco Estuary Institute: Richmond.

A multiyear water quality performance study of a bioretention rain garden located along a major urban transit corridor east of San Francisco Bay was conducted to assess the efficacy of bioretention rain gardens to remove pollutants. Based on data collected in three years between 2012 and 2017, polychlorinated biphenyls (PCBs) and suspended sediment concentrations (SSCs) were reduced (>90%), whereas total mercury (Hg), methylmercury (MeHg), and copper (Cu) were moderately captured (37%, 49%, and 68% concentration reduction, respectively). Anthropogenic microparticles including microplastics were retained by the bioretention rain garden, decreasing in concentration from 1.6 particles/L to 0.16 particles/L. Based on subsampling at 50- and 150-mm intervals in soil cores from two areas of the unit, PCBs, Hg, and MeHg were all present at the highest concentrations in the upper 100 mm in the surface media layers. Based on residential screening concentrations, the surface media layer near the inlet would need to be removed and replaced annually, whereas the rest of the unit would need replacement every 8 years. The results of this study support the use of bioretention in the San Francisco Bay Area as one management option for meeting load reductions required by San Francisco Bay total maximum daily loads, and provide useful data for supporting decisions about media replacement and overall maintenance schedules.

 (627.7 KB) (4.92 MB)
Sutton, R.; Xie, Y.; Moran, K. D.; Teerlink, J. 2019. Occurrence and Sources of Pesticides to Urban Wastewater and the Environment. In Pesticides in Surface Water: Monitoring, Modeling, Risk Assessment, and Management. Pesticides in Surface Water: Monitoring, Modeling, Risk Assessment, and Management. American Chemical Society: Washington, DC. pp 63-88.

Municipal wastewater has not been extensively examined as a pathway by which pesticides contaminate surface water, particularly relative to the well-recognized pathways of agricultural and urban runoff. A state-of-the-science review of the occurrence and fate of current-use pesticides in wastewater, both before and after treatment, indicates this pathway is significant and should not be overlooked. A comprehensive conceptual model is presented to establish all relevant pesticide-use patterns with the potential for both direct and indirect down-the-drain transport. Review of available studies from the United States indicates 42 pesticides in current use. While pesticides and pesticide degradates have been identified in wastewater, many more have never been examined in this matrix. Conventional wastewater treatment technologies are generally ineffective at removing pesticides from wastewater, with high removal efficiency only observed in the case of highly hydrophobic compounds, such as pyrethroids. Aquatic life reference values can be exceeded in undiluted effluents. For example, seven compounds, including three pyrethroids, carbaryl, fipronil and its sulfone degradate, and imidacloprid, were detected in treated wastewater effluent at levels exceeding U.S. Environmental Protection Agency (US EPA) aquatic life benchmarks for chronic exposure to invertebrates. Pesticides passing through wastewater treatment plants (WWTPs) merit prioritization for additional study to identify sources and appropriate pollution-prevention strategies. Two case studies, diazinon and chlorpyrifos in household pesticide products, and fipronil and imidacloprid in pet flea control products, highlight the importance of identifying neglected sources of environmental contamination via the wastewater pathway. Additional monitoring and modeling studies are needed to inform source control and prevention of undesirable alternative solutions.

Wu, J.; Kauhanen, P.; Hunt, J. A.; Senn, D.; Hale, T.; McKee, L. J. . 2019. Optimal Selection and Placement of Green Infrastructure in Urban Watersheds for PCB Control. Journal of Sustainable Water in the Built Environment 5 (2) . SFEI Contribution No. 729.

San Francisco Bay and its watersheds are polluted by legacy polychlorinated biphenyls (PCBs), resulting in the establishment of a total maximum daily load (TDML) that requires a 90% PCB load reduction from municipal stormwater. Green infrastructure (GI) is a multibenefit solution for stormwater management, potentially addressing the TMDL objectives, but planning and implementing GI cost-effectively to achieve management goals remains a challenge and requires an integrated watershed approach. This study used the nondominated sorting genetic algorithm (NSGA-II) coupled with the Stormwater Management Model (SWMM) to find near-optimal combinations of GIs that maximize PCB load reduction and minimize total relative cost at a watershed scale. The selection and placement of three locally favored GI types (bioretention, infiltration trench, and permeable pavement) were analyzed based on their cost and effectiveness. The results show that between optimal solutions and nonoptimal solutions, the effectiveness in load reduction could vary as much as 30% and the difference in total relative cost could be well over $100 million. Sensitivity analysis of both GI costs and sizing criteria suggest that the assumptions made regarding these parameters greatly influenced the optimal solutions. 

If you register for access to the journal, then you may download the article for free through July 31, 2019.

DOI: 10.1061/JSWBAY.0000876

 (3.11 MB)
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.
 (3.37 MB)
Wu, J.; McKee, L. 2019. Regional Watershed Model Implementation Plan. SFEI Contribution No. 943. San Francisco Estuary Institute: Richmond, CA.
 (2.31 MB)
Beagle, J.; Lowe, J.; McKnight, K.; Safran, S. M.; Tam, L.; Szambelan, S. Jo. 2019. San Francisco Bay Shoreline Adaptation Atlas: Working with Nature to Plan for Sea Level Rise Using Operational Landscape Units. SFEI Contribution No. 915. SFEI & SPUR: Richmond, CA. p 255.

As the climate continues to change, San Francisco Bay shoreline communities will need to adapt in order to build social and ecological resilience to rising sea levels. Given the complex and varied nature of the Bay shore, a science-based framework is essential to identify effective adaptation strategies that are appropriate for their particular settings and that take advantage of natural processes. This report proposes such a framework—Operational Landscape Units for San Francisco Bay.

Printed copies available for purchase from Amazon.

 (259.64 MB) (84.6 MB) (20.93 MB)
 (1.43 MB)
Hagerty, S.; Spotswood, E.; McKnight, K.; Grossinger, R. M. 2019. Urban Ecological Planning Guide for Santa Clara Valley. SFEI Contribution No. 941. San Francisco Estuary Institute: Richmond, CA.

This document provides some of the scientific foundation needed to guide planning for urban biodiversity in the Santa Clara Valley region, grounded in an understanding of landscape history, urban ecology and local setting. It can be used to envision the ecological potential for individual urban greening projects, and to guide their siting, design and implementation. It also can be used to guide coordination of projects across the landscape, with the cooperation of a group of stakeholders (such as multiple agencies, cities and counties). Users of this report may include a wide range of entities, such as local nonprofits, public agencies, city planners, and applicants to the Open Space Authority’s Urban Open Space Grant Program.
 (42.6 MB)
Lowe, S. 2019. West Valley Watershed Assessment 2018: Baseline Ecological Condition Assessment of Southwest San Francisco Bay Creeks in Santa Clara County; Calabazas, San Tomas Aquino, Saratoga, Sunnyvale East and West. Salomon, M., Pearce, S., Josh Collins, Titus, D., Eds.. SFEI Contribution No. 944. San Francisco Estuary Institute: Richmond.

This report describes baseline information about the amount and distribution of aquatic resources, and evaluates the overall ecological conditions of streams using the California Rapid Assessment Method (CRAM), for the West Valley watershed in Santa Clara County; consisting of Sunnyvale East and West Channels, Calabazas Creek, San Tomas Aquino and Saratoga creeks, and many smaller tributaries.

 (5.02 MB)
 (9.17 MB)
2018
Yee, D. 2018. 2017 RMP Bay Margins Sediment Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
 (210.1 KB)
Yee, D. 2018. 2017 RMP Water Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
 (212.28 KB)
 (1.13 MB)
 (1.16 MB)
Trowbridge, P. 2018. 2018 Bay RMP Multi-Year Plan. SFEI Contribution No. 860. San Francisco Estuary Institute : Richmond, CA.
 (3.88 MB)
Salop, P.; Shimabuku, I.; Davis, J.; Franz, A. 2018. 2018 Bivalve Retrieval Cruise Report. SFEI Contribution No. 920. San Francisco Estuary Institute : Richmond, CA.
 (248.52 KB)
 (4.48 MB)
Davis, J. 2018. 2018 Regional Monitoring Program Update. SFEI Contribution No. 906. San Francisco Estuary Institute : Richmond, CA.
 (30.3 MB)
Trowbridge, P.; Wong, A.; Davis, J.; Ackerman, J. 2018. 2018 RMP Bird Egg Monitoring Sampling and Analysis Plan. SFEI Contribution No. 891. San Francisco Estuary Institute: Richmond, CA.
 (882.63 KB)
Shimabuku, I.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Bivalve Deployment Cruise Plan. SFEI Contribution No. 892. San Francisco Estuary Institute: Richmond, CA.
 (268.38 KB)
Salop, P. 2018. 2018 RMP Bivalve Deployment Cruise Report. SFEI Contribution No. 903. San Francisco Estuary Institute : Richmond, CA.
 (846.17 KB)
Shimabuku, I.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Bivalve Retrieval Cruise Plan. SFEI Contribution No. 893. San Francisco Estuary Institute: Richmond, CA.
 (466.59 KB)
Shimabuku, I.; Trowbridge, P.; Salop, P.; Franz, A. 2018. 2018 RMP Bivalve Retrieval Cruise Plan. SFEI Contribution No. 893. San Francisco Estuary Institute : Richmond, CA.
 (466.59 KB)
Salop, P.; Franz, A. 2018. 2018 RMP Sediment Cruise Report. SFEI Contribution No. 907. San Francisco Estuary Institute : Richmond, CA.
 (1014.5 KB)
Franz, A.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Sediment Sampling and Analysis Plan. SFEI Contribution No. 904. San Francisco Estuary Institute: Richmond, CA.
 (1.7 MB)
Lin, D.; Sutton, R. 2018. Alternative Flame Retardants in San Francisco Bay: Synthesis and Strategy. SFEI Contribution No. 885. San Francisco Estuary Institute : Richmond, CA.
 (298.68 KB)
Jabusch, T.; Trowbridge, P.; Wong, A.; Heberger, M. 2018. Assessment of Nutrient Status and Trends in the Delta in 2001–2016: Effects of drought on ambient concentrations and trends. SFEI Contribution No. 865. Aquatic Science Center: Richmond, CA.

Nutrients and the effects of nutrients on water quality in the Sacramento-San Joaquin Delta is a priority focus area for the Delta Regional Monitoring Program (Delta RMP). The Program’s first assessment question regarding nutrients is: “How do concentrations of nutrients (and nutrient-associated parameters) vary spatially and temporally?” In this analysis, we confirmed previously reported declining trends in the San Joaquin River for nutrient concentrations at Vernalis and chlorophyll-a concentrations at Buckley Cove and Disappointment Slough. A slight increasing trend for dissolved oxygen at Buckley Cove was also detected which could be confirmation that management actions for the San Joaquin River Dissolved Control Program are having the desired effect. Finally, at stations in Suisun Bay, the Confluence region, and Franks Tract, chlorophyll-a showed modest increasing trends, which were not evident in previous analyses. The new analyses presented in this report and the findings from earlier reports constitute encouraging early progress toward answering the Delta RMP’s assessment questions. Specifically, due to the existence of long-term data sets and synthesis efforts, spatial and temporal trends in the concentrations of nutrients and nutrient-related parameters are reasonably well understood and so are the magnitudes of the most important sources of nutrients from outside the Delta. However, additional synthesis work could be done to understand the factors behind these trends. Large knowledge gaps remain about nutrient sinks, sources, and processes within the Delta. The mechanistic, water quality-hydrodynamic models being developed for the Delta may be able to address these questions in the future.

 (8.33 MB)
Shimabuku, I.; Trowbridge, P.; Sun, J. 2018. Bay 2017 Bay RMP Field Sampling Report. SFEI Contribution No. 849. San Francisco Estuary Institute : Richmond, CA.
 (7.01 MB)
Gilbreath, A.; Pearce, S.; Shimabuku, I.; McKee, L. 2018. Bay Area Green Infrastructure Water Quality Synthesis. SFEI Contribution No. 922. San Francisco Estuary Institute : Richmond, CA.
 (2.31 MB) (1.95 MB)
Beller, E. E.; Spotswood, E.; Robinson, A.; Anderson, M. G.; Higgs, E. S.; Hobbs, R. J.; Suding, K. N.; Zavaleta, E. S.; Grenier, L.; Grossinger, R. M. 2018. Building Ecological Resilience in Highly Modified Landscapes.

Ecological resilience is a powerful heuristic for ecosystem management in the context of rapid environmental change. Significant efforts are underway to improve the resilience of biodiversity and ecological function to extreme events and directional change across all types of landscapes, from intact natural systems to highly modified landscapes such as cities and agricultural regions. However, identifying management strategies likely to promote ecological resilience remains a challenge. In this article, we present seven core dimensions to guide long-term and large-scale resilience planning in highly modified landscapes, with the objective of providing a structure and shared vocabulary for recognizing opportunities and actions likely to increase resilience across the whole landscape. We illustrate application of our approach to landscape-scale ecosystem management through case studies from two highly modified California landscapes, Silicon Valley and the Sacramento–San Joaquin Delta. We propose that resilience-based management is best implemented at large spatial scales and through collaborative, cross-sector partnerships.

 (4.93 MB)
 (1.33 MB)
Yee, D.; Wong, A.; Hetzel, F. 2018. Current Knowledge and Data Needs for Dioxins in San Francisco Bay. SFEI Contribution No. 926. San Francisco Estuary Institute : Richmond, CA.
 (3.06 MB)
Jabusch, T.; Trowbridge, P.; Heberger, M.; Orlando, J.; De Parsia, M.; Stillway, M. 2018. Delta Regional Monitoring Program Annual Monitoring Report for Fiscal Year 2015–16: Pesticides and Toxicity. SFEI Contribution No. 864. Aquatic Science Center: Richmond, CA.

The primary purpose of this report is to document the first year (FY15/16) of pesticide monitoring by the Delta Regional Monitoring Program (Delta RMP). This document reports the results from samples collected monthly from July 2015 through June 2016. The data described in this report are available for download via the California Environmental Data Exchange Network (CEDEN) website.

Pesticide monitoring of the Delta RMP includes chemical analysis and toxicity testing of surface water samples. The parameters analyzed include 154 current use pesticides, dissolved copper, field parameters, and “conventional” parameters (ancillary parameters measured in the laboratory, such as dissolved/particulate organic carbon and hardness). Toxicity tests included an algal species (Selenastrum capricornutum, also known as Raphidocelis subcapitata), an invertebrate (Ceriodaphnia dubia, a daphnid or water flea), and a fish species (Pimephales promelas, fathead minnow). Toxicity testing included the evaluation of acute (survival) and chronic (growth, reproduction, biomass) toxicity endpoints. The surface water samples were collected from 5 fixed sites representing key inflows to the Delta that were visited monthly: Mokelumne River at New Hope Road, Sacramento River at Hood, San Joaquin River at Buckley Cove, San Joaquin River at Vernalis, and Ulatis Creek at Brown Road.

A total of 52 pesticides were detected above method detection limits (MDLs) in water samples (19 fungicides, 17 herbicides, 9 insecticides, 6 degradates, and 1 synergist). A total of 9 pesticides (5 herbicides, 3 insecticides, and 1 degradate) were detected in suspended sediments in 10 of a total of 60 samples collected during the study period. All collected samples contained mixtures of pesticides ranging from 2 to 26 pesticides per sample. From a total of 154 target parameters, 100 compounds were never detected in any of the samples.

 (1.34 MB) (519.77 KB) (2.07 MB) (1.19 MB) (339.08 KB) (26.29 MB) (57.12 MB) (298.4 KB) (3.5 MB) (312.86 KB) (24.34 KB) (180.15 KB) (718.56 KB)
Jabusch, T.; Trowbridge, P.; Heberger, M.; Guerin, M. 2018. Delta Regional Monitoring Program Nutrients Synthesis: Modeling to Assist Identification of Temporal and Spatial Data Gaps for Nutrient Monitoring. SFEI Contribution No. 866. Aquatic Science Center: Richmond, CA.

Nutrient loads are an important water quality management issue in the Sacramento-San Joaquin Delta (Delta) and there is consensus that the current monitoring activities do not collect all the information needed to answer important management questions. The purpose of this report is to use hydrodynamic model outputs to refine recommendations for monitoring nutrients and related conditions in the Delta. Two types of modeling approaches were applied: 1) volumetric water source analysis to evaluate the mix of source waters within each subregion; and 2) particle tracking simulations.The analysis revealed that each Delta subregion has a unique “fingerprint” in terms of how much of its water comes from different sources. Three major recommendations for a future monitoring design were derived from this analysis:

Recommendation #1: The subregions proposed for status and trends monitoring in a previous report should be redrawn to better reflect the mixtures of source waters.

Recommendation #2: Long-term water quality stations are needed in the North Delta, Eastside, and South Delta subregions.

Recommendation #3: Areas with a long-residence time and where mixing of different water sources occurs are potential for nutrient transformation hotspots. High-frequency water quality mapping of these areas has the

 (3.81 MB) (1 MB) (1.69 MB) (1.75 MB) (1.83 MB) (17.97 MB)
 (4.47 MB)
Denslow, N.; Kroll, K.; Mehinto, A.; Maruya, K. 2018. Estrogen Receptor In Vitro Assay Linkage Studies. SFEI Contribution No. 888. San Francisco Estuary Institute : Richmond, CA.
 (1.8 MB)
Shimabuku, I.; Pearce, S.; Trowbridge, P.; Franz, A.; Yee, D.; Salop, P. 2018. Field Operations Manual for the Regional Monitoring Program. SFEI Contribution No. 902. San Francisco Estuary Institute: Richmond, CA.
 (1.43 MB)
Wu, J.; Kauhanen, P.; Hunt, J.; McKee, L. 2018. Green Infrastructure Planning for North Richmond Pump Station Watershed with GreenPlan-IT. SFEI Contribution No. 882. San Francisco Estuary Institute: Richmond, CA.
 (1.39 MB)
Wu, J.; Kauhanen, P.; Hunt, J.; McKee, L. 2018. Green Infrastructure Planning for the City of Oakland with GreenPlan-IT. SFEI Contribution No. 884. San Francisco Estuary Institute : Richmond, CA.
 (1.98 MB)
Wu, J.; Kauhanen, P.; Hunt, J.; McKee, L. 2018. Green Infrastructure Planning for the City of Richmond with GreenPlan-IT. SFEI Contribution No. 883. San Francisco Estuary Institute: Richmond, CA.
 (1.82 MB)
Wu, J.; Kauhanen, P.; Hunt, J.; McKee, L. 2018. Green Infrastructure Planning for the City of Sunnyvale with GreenPlan-IT. SFEI Contribution No. 881. San Francisco Estuary Institute : Richmond, CA.
 (2.21 MB)
Kauhanen, P.; Wu, J.; Hunt, J.; McKee, L. 2018. Green Plan-IT Application Report for the East Bay Corridors Initiative. SFEI Contribution No. 887. San Francisco Estuary Institute: Richmond, CA.
 (1.26 MB)
Hale, T.; Sim, L.; McKee, L. J. 2018. GreenPlan-IT Tracker.

This technical memo describes the purpose, functions, and structure associated with the newest addition to the GreenPlan-IT Toolset, the GreenPlan-IT Tracker. It also shares the opportunities for further enhancement and how the tool can operate in concert with existing resources. Furthermore, this memo describes a licensing plan that would permit municipalities to use the tool in an ongoing way that scales to their needs. The memo concludes with a provisional roadmap for the development of future features and technical details describing the tool’s platform and data structures.

 (1.43 MB)
 (2.53 MB)
Jahn, A. 2018. Gut Contents Analysis of Four Fish Species Collected in the San Leandro Bay RMP PCB Study in August 2016. SFEI Contribution No. 900. San Francisco Estuary Institute: Richmond, CA.
 (1.76 MB)
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.

 (14.16 MB)
 (32.2 MB)
 (1.45 MB)
Davis, J. A.; Heim, W. A.; Bonnema, A.; Jakl, B.; Yee, D. 2018. Mercury and Methylmercury in Fish and Water from the Sacramento-San Joaquin Delta: August 2016 – April 2017. SFEI Contribution No. 908. Aquatic Science Center: Richmond, CA.

Monitoring of sport fish and water was conducted by the Delta Regional Monitoring Program (Delta RMP) from August 2016 to April 2017 to begin to address the highest priority information needs related to implementation of the Sacramento–San Joaquin Delta Estuary Total Maximum Daily Load (TMDL) for Methylmercury (Wood et al. 2010). Two species of sport fish, largemouth bass (Micropterus salmoides) and spotted bass (Micropterus punctulatus), were collected at six sampling locations in August and September 2016. The length-adjusted (350 mm) mean methylmercury (measured as total mercury, which is a routinely used proxy for methylmercury in predator fish) concentration in bass ranged from 0.15 mg/kg or parts per million (ppm) wet weight at Little Potato Slough to 0.61 ppm at the Sacramento River at Freeport. Water samples were collected on four occasions from August 2016 through April 2017. Concentrations of methylmercury in unfiltered water ranged from 0.021 to 0.22 ng/L or parts per trillion. Concentrations of total mercury in unfiltered water ranged from 0.91 to 13 ng/L.

Over 99% of the lab results for this project met the requirements of the Delta RMP Quality Assurance Program Plan, and all data were reportable. This data report presents the methods and results for the first year of monitoring. Historic data from the same or nearby monitoring stations from 1998 to 2011 are also presented to provide context. Monitoring results for both sport fish and water were generally comparable to historic observations.

For the next several years, annual monitoring of sport fish will be conducted to firmly establish baseline concentrations and interannual variation in support of monitoring of long-term trends as an essential performance measure for the TMDL. Monitoring of water will solidify the linkage analysis (the quantitative relationship between methylmercury in water and methylmercury in sport fish) in the TMDL. Water monitoring will also provide data that will be useful in verifying patterns and trends predicted by numerical models of mercury transport and cycling being developed for the Delta and Yolo Bypass by the California Department of Water Resources (DWR).

 (4.09 MB)
Jabusch, T.; Trowbridge, P. 2018. Microbial Water Quality at Minimally Human-Impacted Reference Beaches in Northern California. SFEI Contribution No. 858. San Francisco Estuary Institute : Richmond, CA.
 (3.87 MB)
Sun, J. 2018. Non-Targeted Analysis of Water-Soluble Compounds Highlights Overlooked Contaminants and Pathways (Coming Soon). SFEI Contribution No. 905. San Francisco Estuary Institute: Richmond, CA.
 (1.59 MB)
Grieb, T.; Roy, S.; Rath, J.; Stewart, R.; Sun, J.; Davis, J. A. 2018. North Bay Selenium Monitoring Design. SFEI Contribution No. 921. San Francisco Estuary Institute : Richmond, CA.
 (2.08 MB)
 (8.44 MB)
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.
 (3.2 MB)
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.

 (121.7 MB) (43.68 MB)
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.
 (5.55 MB)
McKnight, K.; Dusterhoff, S. D.; Grossinger, R. M.; Askevold, R. A. 2018. Resilient Landscape Vision for the Calabazas Creek, San Tomas Aquino Creek, and Pond A8 Area: Bayland-Creek Reconnection Opportunities. SFEI Contribution No. 870. San Francisco Estuary Institute-Aquatic Science Center: Richmond, CA. p 40.

This report proposes a multi-faceted redesign of the South San Francisco Bay shoreline at the interface with Calabazas and San Tomas Aquino creeks. Recognizing the opportunities presented by changing land use and new challenges, such as accelerated sea-level rise, we explore in this report a reconfigured shoreline that could improve ecosystem health and resilience, reduce maintenance costs, and protect surrounding infrastructure.

 (68.63 MB) (20.14 MB)
Richey, A.; Dusterhoff, S. D.; McKnight, K.; Salomon, M.; Hagerty, S.; Askevold, R. A.; Grossinger, R. M. 2018. Resilient Landscape Vision for Upper Penitencia Creek. SFEI Contribution No. 894. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.
 (67.6 MB) (11.75 MB)
Wu, J.; Trowbridge, P.; Yee, D.; McKee, L.; Gilbreath, A. 2018. RMP Small Tributaries Loading Strategy: Trends Strategy 2018. SFEI Contribution No. 886. San Francisco Estuary Institute : Richmond, CA.
 (1.3 MB)
Lin, D.; Sutton, R.; Sun, J.; Ross, J. 2018. Screening of Pharmaceuticals in San Francisco Bay Wastewater. SFEI Contribution No. 910. San Francisco Estuary Institute : Richmond, CA.
 (1.06 MB)
 (885.48 KB)
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.
 (1.74 MB)
Sun, J.; Davis, J.; Stewart, R. 2018. Selenium in Muscle Plugs of White Sturgeon from North San Francisco Bay, 2015-2017. SFEI Contribution No. 929. San Francisco Estuary Institute : Richmond, CA.
 (2.24 MB)
 (1.76 MB)
Trowbridge, P. 2018. Status & Trends Monitoring Design: 2018 Update. San Francisco Estuary Institute : Richmond, CA.
 (1.13 MB)
Lin, D.; Davis, J. 2018. Support for Sediment Bioaccumulation Evaluation: Toxicity Reference Values for the San Francisco Bay. SFEI Contribution No. 916. San Francisco Estuary Institute : Richmond, CA.
 (317.14 KB)
 (1.22 MB)
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.

 (3.78 MB)
2017
Yee, D. 2017. 2016 RMP Bird Egg Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
 (332.09 KB)
Yee, D. 2017. 2016 RMP Bivalve Samples Quality Assurance Report. San Francisco Estuary Institute : Richmond, CA.
 (284.38 KB)
Fairey, R.; Sigala, M. 2017. 2017 Margins Microplastics Cruise Report. SFEI Contribution No. 848. Coastal Conservancy & Research: Moss Landing, CA.
 (1.95 MB)
Trowbridge, P.; Sun, J.; Franz, A.; Yee, D. 2017. 2017 Margins Sediment Cruise Plan. SFEI Contribution No. 847. San Francisco Estuary Institute : Richmond, CA.
 (919.33 KB)
 (4.26 MB)
RMP. 2017. 2017 RMP Detailed Workplan and Budget. San Francisco Estuary Institute: Richmond, CA.
 (2.27 MB)
RMP. 2017. 2017 RMP Multi-Year Plan. San Francisco Estuary Institute: Richmond, CA.
 (2.14 MB)
Lin, D.; Sun, J.; Yee, D.; Franz, A.; Trowbridge, P.; Salop, P. 2017. 2017 RMP Water Cruise Plan. SFEI Contribution No. 845. San Francisco Estuary Institute : Richmond, CA.
 (3.63 MB)
Salop, P. 2017. 2017 RMP Water Cruise Report. SFEI Contribution No. 846. Applied Marine Sciences: Livermore, CA.
 (1.16 MB)
Trowbridge, P. 2017. 2018 RMP Detailed Workplan and Budget. San Francisco Estuary Institute : Richmond, CA.
 (390.05 KB)
Associates, H. T. Harvey and; San Francisco Estuary Institute (SFEI). 2017. Annotated Bibliography for Sycamore Alluvial Woodland Habitat Mapping and Regeneration Studies Project.

One component of the Sycamore Alluvial Woodland Habitat Mapping and Regeneration Studies Project is this annotated bibliography of existing scientific literature pertaining to California sycamore ecology. This annotated bibliography is a product of an extensive review into documents, mapping efforts, and personal communications, and presents sources that have been determined to be relevant to understanding the factors that influence California sycamore health and regeneration in central California. The annotated bibliography is divided into the following sections by topic: General Ecology; Historical and Present Distribution; Restoration Ecology and Management; Wildlife Ecology; Geomorphology; Hydrology and Soils; and Health and Regeneration. Each item is briefly summarized and its relevance to the project is described. References that fall under multiple categories are cross-referenced within the document. Similarly, key words are indicated or each reference to highlight various subtopics affecting California sycamore ecology.

 (769.62 KB)
Hale, T.; Grosso, C. 2017. Applied Aquatic Science: A Business Plan for EcoAtlas. San Francisco Estuary Institue: Richmond, CA.

The following plan is intended to ensure the continued vitality of the toolset. The plan’s success will depend upon the continued collaboration of the public agencies that have supported the toolset thus far, but it must also integrate principles of resilience as it accounts for the tensions that arise as organizations move in different strategic directions.

 (1.69 MB) (323.4 KB)
 (1.88 MB)
Dusterhoff, S.; Pearce, S.; McKee, L. J. .; Doehring, C.; Beagle, J.; McKnight, K.; Grossinger, R.; Askevold, R. A. 2017. Changing Channels: Regional Information for Developing Multi-benefit Flood Control Channels at the Bay Interface. Flood Control 2.0. SFEI Contribution No. 801. San Francisco Estuary Institute: Richmond, CA.

Over the past 200 years, many of the channels that drain to San Francisco Bay have been modified for land reclamation and flood management. The local agencies that oversee these channels are seeking new management approaches that provide multiple benefits and promote landscape resilience. This includes channel redesign to improve natural sediment transport to downstream bayland habitats and beneficial re-use of dredged sediment for building and sustaining baylands as sea level continues to rise under a changing climate. Flood Control 2.0 is a regional project that was created to help develop innovative approaches for integrating habitat improvement and resilience into flood risk management at the Bay interface. Through a series of technical, economic, and regulatory analyses, the project addresses some of the major elements associated with multi-benefit channel design and management at the Bay interface and provides critical information that can be used by the management and restoration communities to develop long-term solutions that benefit people and wildlife.

This Flood Control 2.0 report provides a regional analysis of morphologic change and sediment dynamics in flood control channels at the Bay interface, and multi-benefit management concepts aimed at bringing habitat restoration into flood risk management. The findings presented here are built on a synthesis of historical and contemporary data that included input from Flood Control 2.0 project scientists, project partners, and science advisors. The results and recommendations, summarized below, will help operationalize many of the recommendations put forth in the Baylands Ecosystem Habitat Goals Science Update (Goals Project 2015) and support better alignment of management and restoration communities on multi-benefit bayland management approaches.

 (62.69 MB) (23.02 MB)
Yee, D.; Wong, A.; Shimabuku, I.; Trowbridge, P. 2017. Characterization of Sediment Contamination in Central Bay Margin Areas. SFEI Contribution No. 829. San Francisco Estuary Institute: Richmond, CA.
 (2.89 MB)
Trowbridge, P. 2017. Charter: Regional Monitoring Program for Water Quality in San Francisco Bay. SFEI Contribution No. 844. San Francisco Estuary Institute : Richmond, CA.
 (1.68 MB)
 (3.08 MB)
 (14.6 MB)
 (1.42 MB)
 (5.51 MB)
 (47.56 MB)
Robinson, A.; Beagle, J.; Safran, S. M.; McKnight, K.; Grenier, J. Letitia; Askevold, R. A. 2017. Delta Landscapes: A Delta Renewed User Guide. SFEI Contribution No. 854.

A Delta Renewed User Guide aims to increase the accessibility of the technical findings in A Delta Renewed for easier application to restoration and conservation efforts across the Delta. The recommendations in A Delta Renewed focus on landscape-scale ecological guidance. We present three examples of how the information in A Delta Renewed might be used to address different management and restoration questions. Because of the complexity of the Delta system, this guide does not address all possible questions and does not replace the need for detailed, site-specific data and expertise. Rather, it shows how the information in A Delta Renewed might provide a common foundation for restoration planning.

The User Guide was written for a broad audience, including restoration practitioners, landowners, and local, state and federal agencies. The guide provides a step-by-step path through A Delta Renewed; a user is walked through how to apply the findings of the report via a series of steps to address each of the three restoration and management questions. This process is intended to help the user access regionally-specific recommendations and strategies to plan and manage future Delta landscapes that can support desired ecological functions over the long term.


The goal of A Delta Renewed and this guide is not to recreate the Delta of the past. Rather, the objective is to understand how we can re-establish or mimic important natural processes and patterns within this altered system to support desirable ecological functions (such as healthy native fish populations, a productive food web, and support for endangered species), now and into the future.

 (28.86 MB)
 (23.99 MB)