A precursor to SFEI, known as the Aquatic Habitat Institute, was formed in 1986, after several years of discussion among organizations interested in pollutants and pollutant effects in the Estuary. Substantial contention existed at that time among water quality regulatory agencies, dischargers, and environmental advocates over the condition of the Estuary and the importance of contamination in the decline of aquatic resources. Representatives of these interests believed that management of the Estuary would be enhanced if all sides in debates over water quality policy had access to sound, objective scientific information about pollutants and pollutant effects in the Estuary. AHI was created with a broadly representative board of directors, and charged with developing scientific information valuable to water quality managers, but was prohibited from recommending water quality policies. AHI was instrumental in synthesizing existing information about pollution and pollution effects for the State Water Resources Control Board D.1485 Bay Delta Hearings and for the San Francisco Estuary Partnership, (SFEP) established through the Clean Water Act.
AHI was transformed into the San Francisco Estuary Institute (SFEI) in 1993, responding, in part, to the call in the Comprehensive Conservation and Management Plan (CCMP) developed by the San Francisco Estuary Partnership for a comprehensive, coordinated Regional Monitoring and Research Strategy to assess the chemical, physical and biological health of the Estuary. The other motivating force was a realization by AHI’s staff and Board of Directors of changes needed in order for the Institute to recognize its potential. These changes included adopting a more holistic approach to “health of the Estuary” beyond pollutant stressors on aquatic resources and creating a different organizational structure to enable the Institute to actually conduct monitoring and research programs, rather than deal entirely with compiling and synthesizing existing information. A new governance structure was formed, and the new name of the organization, San Francisco Estuary Institute, signified an anticipation of a close working relationship with the San Francisco Estuary Partnership.
While dedicated funding for implementing a comprehensive monitoring and research strategy for the Estuary has not yet materialized, over time, the Institute has strengthened its ties to the Estuary Partnership. SFEI has continued to develop programs that fit within the framework of a comprehensive monitoring and research program as envisioned by the CCMP, but has done so through obtaining grants and contracts from a broad array of federal, state, local and private sources.