Josh Collins's picture

Joshua N. Collins, PhD

Chief Scientist
510-384-0740

Josh Collins is the Lead Scientist at SFEI. He oversees the development and integration of SFEI’s scientific work. Dr. Collins is a landscape ecologist and regional ecological planner with special expertise in mapping and assessing stream and wetland ecosystems. He received his Doctorate in Entomological Sciences at the University of California at Berkeley and did post-doctoral work in Geography and Ecology at the UC Berkeley and UC Davis. As an ecologist in the public utilities industry, Dr. Collins assessed the impacts of power plants on marine, estuarine, and riverine ecosystems. As a consulting ecologist in private practice, he designed stream and wetland restoration projects and developed methods to assess their performance. Since joining SFEI, Dr. Collins has initiated continuing programs in wetland science, watershed science, historical ecology, and regional GIS. He is a leader for a variety of efforts in the West to set long range ecological goals and he has been instrumental in the development of wetland and stream monitoring and assessment methods for California and the nation. Among his many current advisory roles, Dr. Collins chairs the technical team supporting California’s new wetland and riparian area protection policy.

Related Projects, News, and Events

EcoAtlas (Project)

California's EcoAtlas provides access to information for effective wetland management. EcoAtlas is a set of tools for generating, assembling, storing, visualizing, sharing, and reporting environmental data and information. The tools can be used individually or together, and they can be adjusted or tuned to meet the specific needs of environmental planners, regulators, managers, scientists, and educators. The maps and tools can be used to create a complete picture of aquatic resources in the landscape by integrating stream and wetland maps, restoration information, and monitoring results with land use, transportation, and other information important to the state’s wetlands.

Delta Aquatic Resource Inventory (Project)

DARI is the Delta Aquatic Resources Inventory of surface waters, wetlands and other aquatic resources in the Sacramento-San Joaquin Delta (Delta). The goal of the DARI project is to develop a geospatial inventory of aquatic resources that will be used as a common base map for the Delta. A similar mapping approach used to create the California Aquatic Resource Inventory (CARI) will be applied to provide a map of the aquatic resources and their associated attributes.

Bay Area Aquatic Resource Inventory (BAARI) (Project)

The Bay Area Aquatic Resources Inventory (BAARI) is a GIS base map of the Bay Area's wetlands, open water, streams, ditches, tidal marshes and flats, and riparian areas. BAARI was developed using standardized mapping protocols to ensure that the level of detail and wetland classification system is standardized across the region. 

Coyote Creek Watershed Historical Ecology Study (Project)

This report synthesizes historical evidence into a picture of how Coyote Creek looked and functioned before intensive modification. Prepared for the Santa Clara Valley Water District, the report helps explain contemporary landscape conditions and identify options for watershed restoration, natural flood protection, and integrated water management.

Santa Clara Valley Water District Priority D5 Project's Watershed Condition Assessments (2010 to 2018) (Project)

SFEI and the Santa Clara Valley Water District's (Valley Water) Priority D-5 Project have been conducting baseline ecological condition assessments in Santa Clara County, CA to characterize the distribution and abundance of stream and wetlands in five major watersheds, and assess the overall ecological condition of streams in the watersheds based on the California Rapic Assessment Method for streams (CRAM).  The surveys employ the state's recommended Wetland and Riparian Area Monitoring Plan's aproach that includes the use of GIS-base maps of aquatice resources (BAARI), and spatially-balanced ambient stream surveys using CRAM.

Napa River Watershed Profile (Project)

SFEI partnered with the Napa County Resource Conservation District and the Napa County Farm Bureau to develop a watershed-based framework for addressing agricultural management challenges related to improving the health of the Napa River ecosystem. In particular, the project sought to identify possible adaptive management measures that could allow the State Water Board to declare the Napa River unimpaired under section 303(d) of the US Clean Water Act.

California Rapid Assessment Method (CRAM) (Project)

CRAM is a standardized, scientifically defensible rapid assessment method for monitoring the ecological conditions of wetlands throughout California. Because it is standardized, one can compare ecological conditions of wetlands locally, regionally and statewide.

Statewide Wetland Tracking, Science, and Policy Development Support (Project)

SFEI’s Wetland Science Focus Area’s Director, Josh Collins, is a leader in the coordination of statewide science advisory teams and acquiring funding to develop monitoring and assessment tools that support the State’s Wetland and Riparian Area Protection Policy.

SFEI is working with the Santa Clara Valley Water District to develop multi-benefit management tools (News)

In 2014, SFEI and the Santa Valley Water District launched a collaborative partnership aimed at sharing experience, knowledge and resources, and working toward a shared vision of watershed management. Through this partnership, the District has asked SFEI to develop a set of online tools to: 1) identify opportunities for multi-benefit management actions in and along the channels managed by the District; and 2) track the impacts of those actions towards meeting established management targets.

State of the Estuary Conference on Twitter (Event)

In an event convened by the San Francisco Estuary Partnership, SFEI contributed its own intellectual labor to the State of the Estuary Conference. Letitia Grenier served as the lead scientist for the State of the Estuary Report, unveiled at the gathering, and SFEI's scientists and technologists were featured prominently in the program on subjects ranging from nutrients to landscape resilience to green infrastructure to data and tools. By all measures, it was a successful conference.

Developing a Sustainable Business Model for the EcoAtlas Toolset (Project)

This project is funded by a USEPA wetland development grant (2015-2017) to develop a recommended funding and business model for the EcoAtlas toolset.   EcoAtlas is a framework and toolset recommended in the State's Wetland and Riparian Area Monitoring Plan (WRAMP) of the California Wetland Monitoring Workgroup (CWMW). The tools enable users to visualize and assess the distribution, abundance, diversity, and condition of surface waters in a landscape or watershed context.  The Business Plan project is developing several overview and planning memos and a final, compiled recommendation for an EcoAtlas business plan. Those documents are made available here as they are completed.

Dashboards track cumulative benefits on the landscape (News)

EcoAtlas dashboards are comprehensive views of qualified information provided by Project Tracker and the California Aquatic Resource Inventory (CARI). These dynamic visualizations help measure the cumulative benefits of public policies and programs for California's aquatic resources. 

Design by Linda Wanczyk

RipZET: A GIS-based Tool for Estimating Riparian Zones (Project)

The Riparian Zone Estimator Tool (RipZET) is a decision support tool developed by the San Francisco Estuary Institute and Aquatic Science Center for the California Riparian Habitat Joint Venture and the California Water Resources Control Board to assist in the visualization and characterization of riparian areas in the watershed context.

North Bay Mercury Biosentinel Monitoring (Project)

In 2011-2014 SFEI and UC Davis developed and implemented a multi-species biosentinel monitoring approach as an effective and efficient way of monitoring methylmercury exposure in wetland restoration projects across the North Bay. The monitoring design for this project was developed with input from a Science Advisory Group (SAG) of regional and national experts and input from local stakeholders, in order to build a design that would address questions of management concern.

Petaluma Valley Historical Hydrology and Ecology Study (Project)

This project reconstructs the historical hydrology and ecology of the Petaluma River watershed prior to major Euro-American modification. It demonstrates the efficacy of historical hydrology and ecology in identifying and prioritizing multi-benefit restoration opportunities.

Russian River Watershed Projects at the San Francisco Estuary Institute (Project)

Our projects in the Russian River Watershed help us to understand our past, understand our present, and envision our future. Learn more about what SFEI is doing in partnership with others to advance our scientific understanding of this valuable landscape.

Russian River Watershed Atlas helps track and coordinate post-fire activities (News)

Fire recovery in the Russian River Watershed will benefit from a common online platform for compiling, visualizing, and interpreting many kinds of environmental data available from diverse federal, state, regional, and local sources. Providing such a platform is one objective of the Russian River Regional Monitoring Program (R3MP).

Baylands Ecosystem Habitat Goals Project (Project)

SFEI's Letitia Grenier served as lead scientist of the Baylands Ecosystem Habitat Goals Project, which yielded a report called The Baylands and Climate Change: What We Can Do. The report is an update to the 1999 Baylands Ecosystem Habitat Goals, which for the first time set comprehensive restoration goals for the San Francisco Bay estuary. Produced by a collaborative of 21 management agencies working with a multi-disciplinary team of over 100 scientists, it synthesizes the latest science—particularly advances in the understanding of climate change and sediment supply—and incorporates projected changes through 2100 to generate new recommendations for achieving and sustaining healthy baylands ecosystems.

New data layers and Landscape Profile mode added to EcoAtlas (News)

New data layers and Landscape Profile mode have been added to EcoAtlas (ecoatlas.org), an online tool for visualizing the abundance, diversity, and condition of wetlands, along with the project activities that are affecting the landscape. Enhancements include:

Lahontan EcoAtlas Development (Project)

This project will create an EcoAtlas user community for the Lahontan region of the Sierra Nevada to develop capacities within the region to apply EcoAtlas through existing local, regional, state, and federal programs to track projects and summarize map-based and rapid assessment information at the watershed scale.