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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.
