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2020
Buzby, N.; Yee, D.; Salop, P.; Foley, M. 2020. 2019 RMP North Bay Selenium Monitoring Sampling and Analysis Plan. SFEI Contribution No. 969. San Francisco Estuary Institute: Richmond, CA.

The goal of monitoring for selenium in the North Bay tissue and water is to identify leading indicators of change to allow prompt management response to signs of increasing impairment. At the 2016 technical workshop, participants reached a consensus that monitoring sturgeon, clams, and water are all needed to answer management questions. Recommendations for long-term monitoring of these three matrices are detailed in the North Bay Monitoring Design document (Grieb et al. 2018). The purpose of this Sampling and Analysis Plan is to clearly document the sampling design, methods, and responsibilities; and to facilitate coordination among project partners.

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Buzby, N.; Yee, D.; Foley, M.; David, J.; Sigala, M.; Bonnema, A. 2020. 2019 Sport Fish Monitoring Sampling and Analysis Plan. SFEI Contribution No. 970. San Francisco Estuary Institute: Richmond, CA.

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) monitors concentrations of contaminants in fish tissue as indicators of bioaccumulation of contaminants in the Bay. In 2019, the RMP will conduct its eighth round of sport fish monitoring by collecting sport fish samples from various locations in the Bay as a part of routine Status and Trends Monitoring. Add-ons to the routine Status and Trends sport fish monitoring design will include archiving for microplastics and fipronil, as well as additional collections of shiner surfperch in Priority Margin Unit areas (PMUs).

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Soberón, F. Sánchez; Sutton, R.; Sedlak, M.; Yee, D.; Schuhmacher, M.; Park, J. - S. 2020. Multi-box mass balance model of PFOA and PFOS in different regions of San Francisco Bay. Chemosphere 252 . SFEI Contribution No. 986.

We present a model to predict the long-term distribution and concentrations of perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) in estuaries comprising multiple intercommunicated sub-embayments. To that end, a mass balance model including rate constants and time-varying water inputs was designed to calculate levels of these compounds in water and sediment for every sub-embayment. Subsequently, outflows and tidal water exchanges were used to interconnect the different regions of the estuary. To calculate plausible risks to population, outputs of the model were used as inputs in a previously designed model to simulate concentrations of PFOA and PFOS in a sport fish species (Cymatogaster aggregata). The performance of the model was evaluated by applying it to the specific case of San Francisco Bay, (California, USA), using 2009 sediment and water sampled concentrations of PFOA and PFOS in North, Central and South regions. Concentrations of these compounds in the Bay displayed exponential decreasing trends, but with different shapes depending on region, compound, and compartment assessed. Nearly stable PFOA concentrations were reached after 50 years, while PFOS needed close to 500 years to stabilize in sediment and fish. Afterwards, concentrations stabilize between 4 and 23 pg/g in sediment, between 0.02 and 44 pg/L in water, and between 7 and 104 pg/g wet weight in fish, depending on compound and region. South Bay had the greatest final concentrations of pollutants, regardless of compartment. Fish consumption is safe for most scenarios, but due to model uncertainty, limitations in monthly intake could be established for North and South Bay catches.

2019
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Yee, D.; Wong, A.; Buzby, N. 2019. Characterization of Sediment Contamination in South Bay Margin Areas. SFEI Contribution No. 962. San Francisco Estuary Institute: Richmond, CA.

The Bay margins (i.e., mudflats and adjacent shallow areas of the Bay) are important habitats where there is high potential for wildlife to be exposed to contaminants. However, until recently, these areas had not been routinely sampled by the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) due to logistical considerations. In 2015, the RMP conducted a spatially-distributed characterization of surface sediment contamination and ancillary characteristics within the RMP-defined Central San Francisco Bay margin areas. This was repeated in 2017 within South Bay, which for this report refers to the area collectively encompassing Upper South Bay (usually just called the “South Bay” segment in the Bay RMP, “Upper” added here to distinguish from the combined area), Lower South Bay, and “Extreme” Lower South Bay (previously named “Southern Sloughs”) margin areas.

Ambient margins data in South Bay provide a context against which the severity of contamination at specific sites can be compared. The baseline data could also be useful in setting targets and tracking improvements in watershed loads and their nearfield receiving waters, or for appropriate assessment of re-use or disposal of dredged sediment. These spatially distributed data also provide improved estimates of mean concentrations and contaminant inventories in margins. Based on data from this study, contamination in the margin areas accounts for 35% of PCB mass in the upper 15 cm of surface sediments in South Bay, which is approximately proportional to the relative area of the margin (34% of the region). In contrast, margins only contain 30% of the mercury mass in South Bay, somewhat less than their proportional area.

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Yee, D.; Gilbreath, A. N.; McKee, L. J. .; Davis, J. A. 2019. Conceptual Model to Support PCB Management and Monitoring in the San Leandro Bay Priority Margin Unit - Final Report. SFEI Contribution No. 928. San Francisco Estuary Institute: Richmond, CA.

The goal of RMP PCB special studies over the next few years is to inform the review and possible revision of the PCB TMDL and the reissuance of the Municipal Regional Permit for Stormwater, both of which are tentatively scheduled to occur in 2020. Conceptual model development for a set of four representative priority margin units will provide a foundation for establishing an effective and efficient monitoring plan to track responses to load reductions, and will also help guide planning of management actions. The Emeryville Crescent was the first PMU to be studied in 2015-2016. The San Leandro Bay PMU is second (2016-2018), Steinberger Slough in San Carlos is third (2018), and Richmond Harbor will be fourth (2018-2019).

This document is Phase Three of a report on the conceptual model for San Leandro Bay. A Phase One report (Yee et al. 2017) presented analyses of watershed loading, initial retention, and long-term fate, including results of sediment sampling in 2016. A Phase Two data report (Davis et al. 2017) documented the methods, quality assurance, and all of the results of the 2016 field study. This Phase Three report is the final report that incorporates all of the results of the 2016 field study, and includes additional discussion of the potential influence of contaminated sites in the
watershed, the results of passive sampling by Stanford researchers and a comparative analysis of long-term fate in San Leandro Bay and the Emeryville Crescent, a section on bioaccumulation, and a concluding section with answers to the management questions that were the impetus for the work.

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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.
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2018
Yee, D. 2018. 2017 RMP Bay Margins Sediment Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
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Yee, D. 2018. 2017 RMP Water Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
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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.
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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.
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Wu, J.; Trowbridge, P.; Yee, D.; McKee, L.; Gilbreath, A. 2018. RMP Small Tributaries Loading Strategy: Modeling and Trends Strategy 2018. SFEI Contribution No. 886. San Francisco Estuary Institute : Richmond, CA.
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2017
Yee, D. 2017. 2016 RMP Bird Egg Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
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Yee, D. 2017. 2016 RMP Bivalve Samples Quality Assurance Report. San Francisco Estuary Institute : Richmond, CA.
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Trowbridge, P.; Sun, J.; Franz, A.; Yee, D. 2017. 2017 Margins Sediment Cruise Plan. SFEI Contribution No. 847. San Francisco Estuary Institute : Richmond, CA.
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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.
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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.
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Yee, D.; Ross, J. 2017. San Francisco Bay California Toxics Rule Priority Pollutant Ambient Water Monitoring Report. SFEI Contribution No. 814. San Francisco Estuary Institute: Richmond.
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Davis, J.; Yee, D.; Fairey, R.; Sigala, M. 2017. San Leandro Bay PCB Study Data Report. SFEI Contribution No. 855. San Francisco Estuary Institute: Richmond, CA.
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2016
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Trowbridge, P. R.; Davis, J. A.; Mumley, T.; Taberski, K.; Feger, N.; Valiela, L.; Ervin, J.; Arsem, N.; Olivieri, A.; Carroll, P.; et al. 2016. The Regional Monitoring Program for Water Quality in San Francisco Bay, California, USA: Science in support of managing water quality. Regional Studies in Marine Science 4.

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is a novel partnership between regulatory agencies and the regulated community to provide the scientific foundation to manage water quality in the largest Pacific estuary in the Americas. The RMP monitors water quality, sediment quality and bioaccumulation of priority pollutants in fish, bivalves and birds. To improve monitoring measurements or the interpretation of data, the RMP also regularly funds special studies. The success of the RMP stems from collaborative governance, clear objectives, and long-term institutional and monetary commitments. Over the past 22 years, high quality data and special studies from the RMP have guided dozens of important decisions about Bay water quality management. Moreover, the governing structure and the collaborative nature of the RMP have created an environment that allowed it to stay relevant as new issues emerged. With diverse participation, a foundation in scientific principles and a continual commitment to adaptation, the RMP is a model water quality monitoring program. This paper describes the characteristics of the RMP that have allowed it to grow and adapt over two decades and some of the ways in which it has influenced water quality management decisions for this important ecosystem.

Hunt, J.; Trowbridge, P.; Yee, D.; Franz, A.; Davis, J. 2016. Sampling and Analysis Plan for 2016 RMP Status and Trends Bird Egg Monitoring. SFEI Contribution No. 827. San Francisco Estuary Institute: Richmond, CA. p 31 pp.
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2015
Yee, D. 2015. 2013 RMP Water Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
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Yee, D. 2015. 2014 RMP Bivalve Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
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Yee, D. 2015. 2014 RMP Sediment Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
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David, N.; Gluchowski, D. C.; Leatherbarrow, J. E.; Yee, D.; McKee, L. J. . 2015. Estimation of Contaminant Loads from the Sacramento-San Joaquin River Delta to San Francisco Bay. Water Environment Research 87 (4), 334-346.

Contaminant concentrations from the Sacramento-San Joaquin River watershed were determined in water samples mainly during flood flows in an ongoing effort to describe contaminant loads entering San Francisco Bay, CA, USA. Calculated PCB and total mercury loads during the 6-year observation period ranged between 3.9 and 19 kg/yr and 61 and 410 kg/yr, respectively. Long-term average PCB loads were estimated at 7.7 kg/yr and total mercury loads were estimated at 200 kg/yr. Also monitored were PAHs, PBDEs (two years of data), and dioxins/furans (one year of data) with average loads of 392, 11, and 0.15/0.014 (OCDD/OCDF) kg/yr, respectively. Organochlorine pesticide loads were estimated at 9.9 kg/yr (DDT), 1.6 kg/yr (chlordane), and 2.2 kg/yr (dieldrin). Selenium loads were estimated at 16 300 kg/yr. With the exception of selenium, all average contaminant loads described in the present study were close to or below regulatory load allocations established for North San Francisco Bay.

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Kerrigan, J. F.; Engstrom, D. R.; Yee, D.; Sueper, C.; Erickson, P. R.; Grandbois, M.; McNeill, K.; Arnold, W. A. 2015. Quantification of Hydroxylated Polybrominated Diphenyl Ethers (OH-BDEs), Triclosan, and Related Compounds in Freshwater and Coastal Systems. PLOS ONE . SFEI Contribution No. 765.

Hydroxylated polybrominated diphenyl ethers (OH-BDEs) are a new class of contaminants of emerging concern, but the relative roles of natural and anthropogenic sources remain uncertain. Polybrominated diphenyl ethers (PBDEs) are used as brominated flame retardants, and they are a potential source of OH-BDEs via oxidative transformations. OH-BDEs are also natural products in marine systems. In this study, OH-BDEs were measured in water and sediment of freshwater and coastal systems along with the anthropogenic wastewater-marker compound triclosan and its photoproduct dioxin, 2,8-dichlorodibenzo-p-dioxin. The 6-OH-BDE 47 congener and its brominated dioxin (1,3,7-tribromodibenzo-p-dioxin) photoproduct were the only OH-BDE and brominated dioxin detected in surface sediments from San Francisco Bay, the anthropogenically impacted coastal site, where levels increased along a north-south gradient. Triclosan, 6-OH-BDE 47, 6-OH-BDE 90, 6-OH-BDE 99, and (only once) 6’-OH-BDE 100 were detected in two sediment cores from San Francisco Bay. The occurrence of 6-OH-BDE 47 and 1,3,7-tribromodibenzo-p-dioxin sediments in Point Reyes National Seashore, a marine system with limited anthropogenic impact, was generally lower than in San Francisco Bay surface sediments. OH-BDEs were not detected in freshwater lakes. The spatial and temporal trends of triclosan, 2,8-dichlorodibenzo-p-dioxin, OH-BDEs, and brominated dioxins observed in this study suggest that the dominant source of OH-BDEs in these systems is likely natural production, but their occurrence may be enhanced in San Francisco Bay by anthropogenic activities.

2014
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