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McKee, L. J. . 2008. Review of sediment gauging studies in Alameda Creek Watershed. SFEI Contribution No. 571. San Francisco Estuary Institute.
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McKee, L.; Peterson, D.; Braud, A.; Foley, M.; Dusterhoff, S.; Lowe, J.; King, A.; Davis, J. 2023. San Francisco Bay Sediment Modeling and Monitoring Workplan. SFEI Contribution No. 1100. San Francisco Estuary Institute: Richmond, CA.

This document was prepared with guidance gained through two RMP Sediment Workgroup workshops held in late 2022 and early 2023. Given the variety of participants involved, this Workplan encompasses interests beyond San Francisco Bay RMP funders. We thank the attendees for their contributions. 

In 2020, the Sediment Workgroup (SedWG) of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) completed a Sediment Monitoring and Modeling Strategy (SMMS) which laid out a conceptual level series of data and information gaps and generally recommended the use of both empirical data collection and modeling tools to answer initial high priority management questions (McKee et al., 2020). At the time, the SMMS promoted the use of surrogates such as time-continuous turbidity measurements for cross-section flux modeling within the Bay without an understanding of existing Bay hydrodynamic models, their strengths, weaknesses, and potential uses for understanding coupled Bay-mudflat-marsh processes. Since then, the Wetland Regional Monitoring Program (WRMP, www.wrmp.org) has generally promoted the use of coupling monitoring and modeling techniques to inform wetlands sediment management decisions. In addition, he completion of the Sediment for Survival report (a RMPEPA funded collaboration) and the further development of sediment conceptual models has also advanced the need for a coupled dynamic modeling and monitoring program that has the capacity to explore more complex management questions (Dusterhoff et al., 2021; SFEI, 2023). Such a program will take time to develop, but will be more cost-efficient and adaptable and allow for more timely answers to pressing questions. 

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McKee, L. J. .; GeoSyntec,. 2006. Review of methods to reduce urban stormwater loads. SFEI Contribution No. 429. San Francisco Estuary Institute: Oakland. p 150xx.
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Mckee, L.; Lowe, J.; Dusterhoff, S.; Foley, M.; Shaw, S. 2020. Sediment Monitoring and Modeling Strategy. Sediment Monitoring and Modeling Strategy. SFEI Contribution No. 1016. San Francisco Estuary Institute: Richmond, CA.
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Mckee, L.; Gilbreath, A.; Sabin, L. 2022. Small Tributaries Pollutants of Concern Reconnaissance Monitoring: Application of Storm-event Loads and Yields-Based and Congener-Based PCB Site Prioritization Methodologies. SFEI Contribution No. 1067.

Stormwater agencies in the San Francisco Bay Area are identifying watershed areas that are polluted with PCBs in order to prioritize management efforts to reduce impairment in the Bay caused by PCBs carried in stormwater. Water sampling during storms has been used to characterize PCB concentrations but management prioritization based on the comparison of concentrations between watersheds is made difficult due to variations in flow and sediment erosion between storms and in relation to varying land use. In addition, identifying PCB source areas within priority watersheds has proven complex and costly. To address these challenges, the San Francisco Bay Regional Monitoring Program (RMP) has developed two new interpretive methods based on storm-event PCB yields (PCBs mass per unit area per unit time) and fingerprints of Aroclors (commercial PCB mixtures) that make existing data more useful for decision-making. 

The objectives of this study were to: 

  • Apply the yield method to the regional stormwater dataset and provide new rankings, 
  • Estimate the presence of Aroclors in samples where congener data are available
  • Evaluate data weaknesses and recommend watersheds to resample, and
  • Classify watersheds into high, medium, and low categories for potential management.
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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.; 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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May, C. L.; Mohan, A.; Plane, E.; Ramirez-Lopez, D.; Mak, M.; Luchinsky, L.; Hale, T.; Hill, K. 2022. Shallow Groundwater Response to Sea-Level Rise: Alameda, Marin, San Francisco, and San Mateo Counties. Pathways Climate Institute and San Francisco Estuary Institute.

The response of shallow groundwater to sea-level rise is a relatively new field of study. For low-lying coastal communities, sea-level rise adaptation efforts must consider the potential for groundwater rise to avoid maladaptation. The need to better understand this slow and chronic threat was identified as a critical data gap in the San Francisco Bay Area’s (Bay Area’s) adaptation efforts during the Bay Area Groundwater and Sea-Level Rise Workshop in 2019.

Pathways Climate Institute LLC (Pathways) and the San Francisco Estuary Institute (SFEI) gathered and analyzed multiple data sets and collaborated with city and county partners to analyze and map the existing “highest annual” shallow groundwater table and its likely response to future sea-level rise. This effort covers four counties (Alameda, Marin, San Francisco, San Mateo) and was funded by the Bay Area Council’s California Resilience Challenge. The study focused on the San Francisco Bay side of each county and does not include the Pacific coastline of Marin, San Francisco, nor San Mateo Counties. An advisory committee composed of city and county representatives provided essential support by gathering data and reviewing depth-to-groundwater maps. Additional academic and agency advisors participated in project team meetings and informed project direction. This effort produced the following publicly available data and online tools to support adaptation efforts:

  • Existing and future condition depth to groundwater GIS data available for download (geodatabase format).
  • A StoryMap providing background information and graphical representations of the processes and impacts of groundwater rise.
  • Web maps showing: (1) existing depth to groundwater; and (2) a comparison of the extent of emergent groundwater to the extent of coastal flooding under various sea-level-rise scenarios.
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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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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.

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Lowe, S. 2017. MS4 2009 Permit Monitoring Results (2010-2015) Summary of Sonoma County Water Agency’s Data for two Sites in Santa Rosa Creek. SFEI Contribution No. 832. San Francisco Estuary Institute: Richmond. CA. p 35.

This memo summarizes the Sonoma County Water Agency's  2009 receiving water monthly monitoring results for the North Coast Regional Water Quality Control Board's NPDES Permit No. R1-2009-0050.  The data were compiled, formatted and uploaded to SFEI’s Regional Data Center and are availble through CEDEN (https://ceden.waterboards.ca.gov/AdvancedQueryTool) under the Program Name "Russian River MS4 Program" and Project Names "2009 5 year Permit for RR_MS4 Program SCWA" and "2009 5 year Permit for RR_MS4 Program CSR".  The memo summarizes field measures and water chemistry, bacteria, and toxiciity results from two receving waters sites in Santa Rosa Creek downstream (C1-SRC-D) and upstream of the City of Santa Rosa.  

This memo was funded by a Suplemental Environmental Project (SEP) settlement of an enforcement action by the North Coast Regional Water Quality Control Board against the County of Sonoma.  2016.

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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. 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. 2020. Santa Clara County Five Watersheds Assessment: A Synthesis of Ecological Data Collection and Analysis Conducted by Valley Water. Pearce, S., Salomon, M., Collins, J., Titus, D., Eds.. SFEI Contribution No. 963. San Francisco Estuary Institute: Richmond. CA. p 71.

This report synthesizes the baseline assessments for Santa Clara County’s five watersheds to present similarities, differences, and compare ecological condition in streams across watersheds and their subregions, San Francisco Bay-Delta ecoregion, and statewide based on CRAM. It also interprets the assessment results and comparisons to identify risks to stream conditions, and opportunities for stream stewardship. Project D5’s baseline assessments establish a monitoring and assessment framework for evaluating the performance of Valley Water’s programs, projects, maintenance activities, and on-the-ground stewardship actions.

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Lowe, S.; Pearce, S.; Collins, J. 2017. A Watershed Approach to Restoration and Mitigation Planning, Monitoring, and Assessment Based on the Wetland and Riparian Area Monitoring Plan (WRAMP): Addendum to the Upper Pajaro River Watershed Assessment 2015. SFEI Contribution No. 818. San Francisco Estuary Institute: Richmond. CA. p 30.

This report demonstrates a possible watershed-based approach to evaluating mitigation sites using the California Rapid Assessment Method (CRAM). The Santa Clara Valley Water District (Valley Water) is leading the Llagas Creek Flood Control Project in the upper Pajaro River watershed, Santa Clara County, CA. Mitigation for the Project involves enhancing riverine wetlands on-site (within the flood control channel) and restoring riverine wetlands and enhancing depressional wetlands at Lake Silveira, in the Llagas Creek watershed. Valley Water is incorporating CRAM into its planning and assessment of mitigation efforts and Valley Water's Priority D.5 Project's Pajaro River Watershed ambient stream condition survey (2015) provided the watershed context for evaluating project conditions against the general ecological conditions of streams within the watershed - employing CRAM. This WRAMP demonstration compared pre-project ecological condition assessments (employing CRAM) from the project's impact and mitigation sites to ambient watershed conditions and estimated the amount of ecological lift expected in the future as a result of the planned mitigation and restoration efforts.

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Lowe, S. 2020. Coyote Creek Watershed Reassessment 2020 Ambient Stream Condition Survey Design and Monitoring Plan: A Review of the Original 2010 Survey Design and Development of the 2020 Reassessment Strategy. Pearce, S., Ed.; Titus, D., Tran.. SFEI Contribution No. 1055. San Francisco Estuary Institute: Richmond. CA. p 18.

This technical report describes the ten-year ambient stream condition reassessment survey design and monitoring plan (or strategy) for the Coyote Creek watershed. Because the reassessment employed (and modified) the 2010 sample draw, essential background information about the original 2010 probability-based survey design, sample draw, and field assessment outcomes were provided.

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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.; Pearce, S. 2022. Building Capacity of the California Wetland Program Plan to Protect and Restore Vernal Pools. SFEI Contribution No. 1087. San Francisco Estuary Institute: Richmond. CA. p 30.

This report describes the updates to the vernal pool habitat map, the development of the ambient baseline ecological condition survey of vernal pool systems within the Central Valley, and the development and results of the habitat development curve. A fictional project example shows how CRAM and the vernal pool complex CDFs and HDCs can help project proponents and the regulatory agencies think critically about project designs (using CRAM Attributes and Metrics as a standard measure), evaluate project conditions within a regional landscape context, and monitor project performance over time to ensure that project goals are met.

Funding for this report was provided through an agreement with the U.S. Environmental Protection Agency (USEPA).  This report does not necessarily reflect the views and policies of USEPA nor does the mention of trade names or commercial products within this report constitute endorsement or recommendation for use.

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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.; Kauhanen, P. 2019. Prioritizing Candidate Green Infrastructure Sites within the City of Ukiah: A Demonstration of the Site Locator Tool of GreenPlan-IT. Report prepared for the City of Ukiah Department of Public Works under Supplemental Environmental Project # R1-018-0024. San Francisco Estuary Institute: Richmond. CA.

This report describes the application of GreenPlan-IT’s Site Locator Tool to identify and rank candidate GI installation sites within the City of Ukiah.  The Site Locator Tool is the first (foundational) tool of the GreenPlan-IT toolkit, meaning that the outputs are required inputs for both the Hydrologic Modeling and Optimization tools.   The Site Locator Tool addresses the question: where are the best locations for GI implementation based on local planning priorities? 

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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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