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

Online 401 Application Tool (Project)

This tool provides a permit negotiation tool for applicants and Regional Water Board staff to work together on preparing a permit for a 401 Water Quality Certification or Waste Discharge Report for projects impacting waters of the US or California. The application tool will streamline 401 Certification applications, provide access to historical 401 cases, and enable standardized reports on the status and trends of 401 projects and ambient conditions for watersheds, regions, and statewide.

Head of Tide (Project)

SFEI completed a pilot study focused on creating a framework for a rapid protocol that can be used to delineate the current and future head of tide zone for San Francisco Bay tributaries using both “desktop” and field investigations.

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.

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.

Tahoe WRAMP Demonstration: Mapping Standards (Project)

The Tahoe WRAMP Demonstration Project implemented detailed and standardized mapping protocols within the Tahoe Basin in two watersheds, based on BAARI mapping standards.  New region specific mapping methodologies were developed to address region specific wetland types. 

North Coast WRAMP Demonstration: Mapping Standards (Project)

The North Coast WRAMP Demonstation Project focused on mapping and assessing the condition of aquatic resources within the Santa Rosa Plain, CA using GIS based mapping protocols consistent with BAARI.  A new regional Mapping Standards Methodology (NCARI) was developed to add regional wetland types not covered in BAARI's documentation. 

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.

Tahoe WRAMP Demonstration: Watershed Assessment (Project)

The Tahoe WRAMP Watershed Demontration Project transfered statewide wetland monitoring and asseement tools to Sierra Nevada environmental agencies and organizations through a pilot project that assessed the distribution and abundance of wetlands, and the overall ecologcial condition of streams in two watersheds within the Lake Tahoe Basin.

Santa Rosa Plain Wetlands Profile: A Demonstration of WRAMP (Project)

The Santa Rosa Plain WRAMP project demonstrated the use of the State’s standardized monitoring and assessment tools in a North Coast watershed setting and described how the results can support watershed based management and planning decisions to protect and manage the state’s wetlands at a landscape scale. 

California Rapid Assessment Method (CRAM): Bar-Built Estuarine Wetlands (Project)

 The CRAM Bar-Built Estuarine module is used for assessing reaches of coastal rivers and streams that are ecologically influenced by seasonal closures of their tidal inlets. 

California Rapid Assessment Method (CRAM): Slope Wetlands (Project)

CRAM is a cost-effective and scientifically defensible rapid assessment method for monitoring and assessing the ecologcial conditions of wetlands throughout California. It takes less than half a day to assess a wetland area, and is designed evaluate the condition of the wetland based on it's landscape setting, hydrology, physical structure and biological structure.  Because the methodology is standardized for over seven types of wetlands, ecological condition scores can be compared at the local, regional and statewide landscape scales.  

Transitional Ecotone Vegetation Data Management System (Project)

Upload and access data from vegetation surveys of intertidal-upland ecotones

Six County Aquatic Resource Inventory (Project)

The US Army Corps of Engineers, Sacramento Division updated wetland and stream maps for the 6 county area (Sacramento, Placer, Yolo, El Dorado, Yuba, and Sutter Counties) to support regulatory, planning, and management efforts in the area.  The map was made public in 2011 and was added to EcoAtlas in 2013.

View the Six County streams data online at EcoAltas.

Recent workshop in the Lahontan region establishes an implementation roadmap for watershed-based decision support tools (News)

SFEI representatives Cristina Grosso and Josh Collins helped to foster the use of EcoAtlas and related tools in the Lahontan region during a recent workshop. The objective of the workshop was to train interested parties inside and outside of the Tahoe Basin on EcoAtlas’ watershed-based decision support tools. The workshop began with a presentation on the applications of watershed-based decision support tools in the regulatory context. A Technical Demo Session and Open Lab provided hands-on training for EcoAtlas’ planning (CARI/TARI, CARI Editor), tracking (Project Tracker), and visualization tools (Landscape Profile Tool).

SFEI featured in 5 major newspaper articles over two weeks (News)

Articles featuring the Pulse of the Bay, the State of the Estuary Report, and SFEI's work on microplastics saturate the news media since Sept 9, 2015.

Recent weeks have demonstrated the tremendous value that SFEI brings not only to the domain of environmental science but also to resource management and the public landscape. The deluge of articles covers a wide breadth of subjects, each with great urgency and relevance to issues of public importance.

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.

Following the State of the Estuary Conference, a newspaper article describes the future of Marin with help from SFEI's Josh Collins and Letitia Grenier (News)

Journalist Mark Prado's article in the Marin Independent Journal reports the mixed picture of health in the San Francisco Estuary. He writes:

“In many regards the bay is as healthy as it has been in a long time,” said San Anselmo native Josh Collins, chief scientist with the San Francisco Estuary Institute. “But some aspects of the bay are slower to heal,” he added. “There are sill longer-lasting pollutants in the bay, but they are not being put in the system anymore.”

Rising seas threaten San Francisco Bay and Delta wetlands and land (News)

Dennis Cuff of the San Jose Mercury News wrote an article on the relationship between the region's wetlands and sea level rise. "Rising seas threaten San Francisco Bay and Delta wetlands and land" introduces Cuff's readers to the State of the Estuary Report, a 100-page document produced by the San Francisco Estuary Partnership with scientific leadership from SFEI. Cuff quotes SFEI's senior scientist Letitia Grenier:

EcoAtlas: New CARI Editor and Modern Delta Habitat Types (News)

An accurate basemap is fundamental to watershed planning and assessments. The California Aquatic Resources Inventory, or CARI, offers such a basemap for aquatic resource identification and classification. But to keep it current and enhance its details, SFEI-ASC must leverage local knowledge. The new CARI Editor promotes regional stewardship and allows users to submit updates, deletions or new features for streams and wetlands.

BAARI v2.0 is now available! (News)

Version 2 of the BAARI (Bay Area Aquatic Resource Inventory) GIS dataset has been released. Local experts provided advice on and reviewed BAARI’s baylands, stream and wetland data layers to increase its accuracy and detail.