The San Francisco Estuary Institute (SFEI) is a 501(c)(3) non-profit organization whose mission is to foster the development of scientific understanding needed to protect and enhance the San Francisco Estuary through research, monitoring, and communication.

SFEI was created in 1993 to help implement the San Francisco Estuary Project's Comprehensive Conservation and Management Plan (CCMP), which seeks to maintain, enhance and protect the ecological integrity of the Estuary. SFEI's offices are located in Oakland, CA on the banks of San Leandro Creek overlooking Arrowhead Marsh.

The Institute conducts research and monitoring in four major programs: Contaminant Monitoring and Research (including the Regional Monitoring Program, RMP), Wetlands, Watersheds, and Biological Invasions. Two other Institute components, Historical Ecology and Information Technology (including the EcoAtlas Information System) augment and support its major programs.

SFEI is funded through contracts and grants from a variety of federal, state, and local agencies and private foundations. SFEI is overseen by a Board of Director's with diverse Bay interests, and employs a staff of 28. SFEI supports the Bay Delta Science Consortium through its program areas, local databases and Geographic Information Systems.