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Results of the Benthic Pilot Study 1994 - 1997, Part 1. SFEI Contribution No. 39. San Francisco Estuary Institute: Richmond, CA.
2000. 
Re-design Process of the San Francisco Estuary Regional Monitoring Program for Trace Substances (RMP) Status & Trends Monitoring Component for Water and Sediment. SFEI Contribution No. 507. San Francisco Estuary Institute: Oakland, CA.
2005. 
Quality Assurance Project Plan: Investigations of Sources and Effects of Pyrethroid Pesticides in Watersheds of the San Francisco Bay Estuary. San Francisco Estuary Institute: Oakland.
2007. 
Estuarine and scalar patterns of invasion in the soft-bottom benthic communities of the San Francisco Estuary. Biological Invasions 5, 85-102 . SFEI Contribution No. 292.
2003. 1999 Quality Assurance Project Plan. SFEI Contribution No. 33. San Francisco Esturary Institute: Oakland.
1999. 
Patterns and trends in sediment toxicity in the San Francisco Estuary. Environmental Research 105, 145-155.
2007. 
Final Project Report: Investigations of Sources and Effects of Pyrethroid Pesticides in Watersheds of the San Francisco Estuary. SFEI Contribution No. 523. San Francisco Estuary Institute: Oakland.
2007. 
2000.
Sediment Conditions near Wastewater Discharges in San Francisco Bay. San Francisco Estuary Institute: Oakland, CA.
1999. San Francisco Estuary Regional Monitoring Program (RMP) Annual Monitoring Results, 2002. SFEI Contribution No. 466. San Francisco Estuary Institute: Oakland, CA.
2004. Assessment of Macrobenthos Response to Sediment Contamination in the San Francisco Estuary (published in Environmental Toxicology and Chemistry). Environmental Toxicology and Chemistry 23, 2178.
2004. Causes of Sediment Toxicity to Mytilus galloprovincialis in San Francisco Bay, California. Archive of Environmental Contamination Toxicology 45, 486-491 . SFEI Contribution No. 296.
2003. San Francisco Estuary National Water Quality Monitoring Network Pilot Study Report. SFEI Contribution No. 548. p 70.
2008. 
Assessment of macrobenthos resonse to sediment contamination in the San Francisco Estuary, USA. Environmental Toxicology and Chemistry 23 . SFEI Contribution No. 60.
2004. 
CISNet San Pablo Bay Network of Environmental Stress Indicators; Benthic Microfauna. SFEI Contribution No. 299. San Francisco Estuary Institute: Oakland, CA.
2003. 2001 Quality Assurance Project Plan: Regional Monitoring Program for Trace Substances. SFEI Contribution No. 33. San Francisco Estuary Institute.
2001. Impacts of Nonindigenous Species on Subtidal Benthic Assemblages in the San Francisco Estuary. SFEI Contribution No. 329. p 16.
1999. Re-design Process of the San Francisco Estuary Regional Monitoring Program for Trace Substances (RMP). SFEI Contribution No. 109. San Francisco Estuary Institute: Oakland, CA.
2004. 
Surveillance for previously unmonitored organic contaminants in the San Francisco Estuary. Marine Pollution Bulletin 46, 1102-1110.
2003. Monitoring Plan Petaluma River Watershed Nutrient and Bacteria Impairment Study: Employing the Reachwide Benthos Method for Stream Algae Sampling and Additional Water Column Nutrient and Fecal Indicator Bacteria Measures. Aquatic Science Center: Oakland, CA.
2010. 
Final Project Report for the Demonstration Project in Three Critical Coastal Area Watersheds. San Francisco Estuary Institute: Richmond, CA.
2011. 
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.
2014. 
Demonstration Watershed Assessment For the Tahoe Basin Using the Wetland & Riparian Area Monitoring Plan. SFEI Contribution No. 703. San Francisco Estuary Institute: Richmond, CA.
2013. 
Project: Statistical Design, Analysis and Guidance on the Pajaro and Lower Peninsula Watershed Assessments. TASK 3: GRTS Survey Designs and Sample Draws Memorandum – Pajaro and Lower Peninsula Watersheds. SFEI Contribution No. 763.
2015. 
Statistical Design, Analysis, and Graphics for the Guadalupe River Watershed Assessment 2012. SFEI Contribution No. 687. San Francisco Estuary Institute: Richmond, CA.
2013. 
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.
2016. 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).

Surveillance for previously unmonitored organic contaminants in the San Francisco Estuary. Marine Pollution Bulletin 46, 1102-1110 . SFEI Contribution No. 295.
2003. 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.
2016. 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).

Lower Peninsula Watershed Condition Assessment 2016: Southwest San Francisco Bay, Santa Clara County, San Francisquito to Stevens Creeks. Technical memorandum prepared for the Santa Clara Valley Water District. . SFEI Contribution No. 809. San Francisco Estuary Institute: Richmond. p 53.
2017. 
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. . SFEI Contribution No. 944. San Francisco Estuary Institute: Richmond.
2019. 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.

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.
2017. 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.

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. . SFEI Contribution No. 1055. San Francisco Estuary Institute: Richmond. CA. p 18.
2020. 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.

Santa Clara County Five Watersheds Assessment: A Synthesis of Ecological Data Collection and Analysis Conducted by Valley Water. . SFEI Contribution No. 963. San Francisco Estuary Institute: Richmond. CA. p 71.
2020. 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.

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.
2019. 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?

Coyote Creek Watershed Reassessment 2020: 10-Year Reassessment of the Ecological Condition of Streams Applying the California Rapid Assessment Method, Santa Clara County, California. SFEI Contribution No. 1043. San Francisco Estuary Institute: Richmond. CA. p 131.
2021. This report describes the amount and distribution of aquatic resources in the Coyote Creek watershed, Santa Clara County, California, and presents the first reassessment of stream ecosystem conditions using a watershed approach and the California Rapid Assessment Method (CRAM). Field work was conducted in 2020, ten years after the baseline watershed assessment completed in 2010.
