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Kramer, K. S. 1989. Inventory of Current Monitoring Programs in the San Francisco Bay and Delta. SFEI Contribution No. 155. San Francisco Estuary Institute: Richmond, CA. p 39.
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Kramer, K. S. 1989. Inventory of Monitoring Programs in the San Francisco Bay and Delta. SFEI Contribution No. 156. AHI: Richmond, CA. p 48.
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Kucera, T.; Breauz, A.; Zielinski, W. 2002. Data Collection Protocol Montioring River Otter (Lutra [=Lontra] canadensis). SFEI Contribution No. 241. CA State University Stanislaus, U.S Forest Service, San Francisco Bay Regional Water Quality Control Board: Oakland, CAStanislaus, CA. p 11.
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Leatherbarrow, J. E.; Yee, D.; Davis, J. A. 2001. PCBs in effluent. SFEI Contribution No. 237.
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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.
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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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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.
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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.
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Livsey, D. N.; Downing-Kunz, M. A.; Schoellhamer, D. H.; Manning, A. J. 2020. Suspended Sediment Flux in the San Francisco Estuary: Part I—Changes in the Vertical Distribution of Suspended Sediment and Bias in Estuarine Sediment Flux Measurements. Estuaries and Coasts . SFEI Contribution No. 990.

In this study, we investigate how changes in the vertical distribution of suspended sediment affect continuous suspended sediment flux measurements at a location in the San Francisco Estuary. Current methods for measuring continuous suspended sediment flux estimates relate continuous estimates of suspended-sediment concentration (SSC) measured at-a-point (SSCpt) to discrete cross-section measurements of depth-averaged, velocity-weighted SSC (SSCxs). Regressions that compute SSCxs from continuous estimates of SSCpt require that the slope between SSCpt and SSCxs, controlled by the vertical distribution of SSC, is fixed. However, in tidal systems with suspended cohesive sediment, factors that control the vertical SSC profile—vertical turbulent mixing and downward settling of suspended sediment mediated by flocculation of cohesive sediment—constantly vary through each tide and may exhibit systematic differences between flood and ebb tides (tidal asymmetries in water velocity or particle size). We account for changes in the vertical SSC profile on estimates of SSCxs using time series of the Rouse number of the Rouse-Vanoni-Ippen equation combined with optical turbidity measurements, a surrogate for SSCpt, to predict SSCxs from 2009 to 2011 and 2013. Time series of the Rouse number were estimated by fitting the Rouse-Vanoni-Ippen equation to SSC estimated from optical-turbidity measurements taken at two elevations in the water column. When accounting for changes in the vertical SSC profile, changes in not only the magnitude but also the direction of cumulative sediment-flux measurements were observed. For example, at a mid-depth sensor, sediment flux estimates changed from − 319 kt (± 65 kt, negative indicating net seaward transport) to 482 kt (± 140 kt, positive indicating net landward transport) for 2009–2011 and from − 388 kt (± 140 kt) to 1869 kt (± 406 kt) for 2013–2016. At the study location, estimation of SSCxs solely from SSCpt resulted in sediment flux values that were underestimates on flood tides and overestimates on ebb tides. This asymmetry is driven by covariance between water velocity and particle settling velocity (Ws) with larger Ws on flood compared to ebb tides. Results of this study indicate that suspended-sediment-flux measurements estimated from point estimates of SSC may be biased if systematic changes in the vertical distribution of SSC are unaccounted for.

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Lowe, S.; Thompson, B.; Kellogg, M. 2000. Results of the Benthic Pilot Study 1994 - 1997, Part 1. SFEI Contribution No. 39. San Francisco Estuary Institute: Richmond, CA.
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Lowe, S.; Thompson, B. 2004. Assessment of macrobenthos resonse to sediment contamination in the San Francisco Estuary, USA. Environmental Toxicology and Chemistry 23 . SFEI Contribution No. 60.
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Lowe, S.; Salomon, M.; Pearce, S. 2016. Lower Peninsula Watershed Condition Assessment 2016. Technical memorandum prepared for the Santa Clara Valley Water District - Priority D5 Project. SFEI Contribution No. 809. San Francisco Estuary Institute: Richmond, CA. p 49.

In 2016 The Santa Clara Valley Water District and its consultants conducted a watershed wide survey to characterize the distribution and abundance of the aquatic resources within the Lower Peninsula watershed wtihin Santa Clara County, CA based on available GIS data, and to assess the overall ecological condition of streams within the watershed based on a statistically based, random sample design and the California Rapid Assessment Method for streams (CRAM).

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Lowe, S.; Hoenicke, R.; Davis, J. A. 1999. 1999 Quality Assurance Project Plan. SFEI Contribution No. 33. San Francisco Esturary Institute: Oakland.
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Lowe, S.; Salomon, M.; Pearce, S.; Josh Collins; Titus, D. 2016. Upper Pajaro River Watershed Condition Assessment 2015. Technical memorandum prepared for the Santa Clara Valley Water District - Priority D5 Project. SFEI Contribution No. 810. San Francisco Estuary Institute: Richmond, CA. p 60.

In 2015 The Santa Clara Valley Water District and it's consultants conducted a watershed wide survey to characterize the distribution and abundance of the aquatic resources within the upper Pajaro River watershed wtihin Santa Clara County, CA based on available GIS datasets, and to assess the overall ecological condition of streams within the watershed based on a statistically based random sample design and the California Rapid Assessment Method for streams (CRAM).

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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.

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Lowe, S.; Josh Collins; Pearce, S. 2013. Statistical Design, Analysis, and Graphics for the Guadalupe River Watershed Assessment 2012. SFEI Contribution No. 687. San Francisco Estuary Institute: Richmond, CA.
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Lowe, S.; Robinson, A.; Frontiera, P.; Cayce, K.; Collins, J. N. 2014. Creating Landscape Profiles of Aquatic Resource Abundance, Diversity and Condition. SFEI Contribution No. 725. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 21.
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Lowe, S.; Ross, J. R. M.; Thompson, B. 2003. CISNet San Pablo Bay Network of Environmental Stress Indicators; Benthic Microfauna. SFEI Contribution No. 299. San Francisco Estuary Institute: Oakland, CA.
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Mason, S. A.; Garneau, D.; Sutton, R.; Chu, Y.; Ehmann, K.; Barnes, J.; Papazissimos, D.; Rogers, D. L. 2016. Microplastic pollution is widely detected in US municipal wastewater treatment plant effluent. Environmental Pollution 218, 1045-1054.

Municipal wastewater effluent has been proposed as one pathway for microplastics to enter the aquatic environment. Here we present a broad study of municipal wastewater treatment plant effluent as a pathway for microplastic pollution to enter receiving waters. A total of 90 samples were analyzed from 17 different facilities across the United States. Averaging all facilities and sampling dates, 0.05 ± 0.024 microparticles were found per liter of effluent. Though a small value on a per liter basis, even minor municipal wastewater treatment facilities process millions of liters of wastewater each day, yielding daily discharges that ranged from ∼50,000 up to nearly 15 million particles. Averaging across the 17 facilities tested, our results indicate that wastewater treatment facilities are releasing over 4 million microparticles per facility per day. Fibers and fragments were found to be the most common type of particle within the effluent; however, some fibers may be derived from non-plastic sources. Considerable inter- and intra-facility variation in discharge concentrations, as well as the relative proportions of particle types, was observed. Statistical analysis suggested facilities serving larger populations discharged more particles. Results did not suggest tertiary filtration treatments were an effective means of reducing discharge. Assuming that fragments and pellets found in the effluent arise from the 'microbeads' found in many cosmetics and personal care products, it is estimated that between 3 and 23 billion (with an average of 13 billion) of these microplastic particles are being released into US waterways every day via municipal wastewater. This estimate can be used to evaluate the contribution of microbeads to microplastic pollution relative to other sources (e.g., plastic litter and debris) and pathways (e.g., stormwater) of discharge.

May, M. D.; Kramer, K. S. 1993. Teaching About the San Francisco Bay and Delta - An Activities and Resource Guide, 2nd Ed. SFEI Contribution No. 174. San Francisco Estuary Institute: Richmond, Ca. p 500.
May, M. 2000. The Pulse of the Estuary: Tracking Contamination with the Regional Monitoring Program 1993-1998. SFEI Contribution No. 100. San Francisco Estuary Institute.
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May, M.; SFEI. 2002. 2000 Pulse of the Estuary: Monitoring and Managing Contamination in the San Francisco Estuary. SFEI Contribution No. 88. San Francisco Estuary Institute: Oakland, CA.
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