The San Pablo Bay National Wildlife Refuge lies along the north shore of San Pablo Bay in Sonoma, Solano, and Napa Counties in northern California. The refuge includes open bay/tidal marsh, mud flats, and seasonal and managed wetland habitats.

The Napa-Sonoma marshes in San Pablo Bay have been greatly impacted by human activities such as hydraulic mining, salt production, water diversions, and diking, draining, and filling for agricultural and industrial uses. About 85 percent of the historic tidal marshes of San Pablo Bay have been altered, negatively affecting the ability of the remaining tidal marshes to accept winter rainfall and purify water in the bay.

The refuge provides critical migratory and wintering habitat for shorebirds and waterfowl, particularly diving ducks, and provides year-round habitat for endangered, threatened, and sensitive species like the California clapper rail, salt marsh harvest mouse, California black rail, San Pablo song sparrow, and Suisun shrew.

Numerous other threatened, endangered, and sensitive species require tidal marsh habitat for their survival, including 11 fish species that swim through San Pablo Bay to reach their fresh water spawning grounds.

Less than 150 years ago, the Napa-Sonoma marshes surrounding San Pablo Bay comprised one of the most extensive wetland systems along the Pacific coast. This system provided habitat for millions of migrating waterfowl and shorebirds as well as resident wildlife. Plants specialized to live in aquatic habitats grew bountifully, sheltering and feeding a rich diversity of species.

Rapid development of the area began with the discovery of gold in the Sierra Nevada foothills in the 1850s. Hydraulic mining operations contributed huge amounts of sediment to the San Francisco Bay Estuary. For the next hundred years, the marshes were filled, diked, or drained to support the bay's development as a major center of commerce.

Today, only 15% of the bay's historic tidal lands remains. Since the 1960s, conservation agencies, non-profit organizations, and local grassroots efforts have worked to protect the Bay. Largely comprised of thousands of acres of tidelands leased from the California State Lands Commission, the refuge's ultimate plans include protection and conservation of more than 20,000 acres of critical wildlife in northern San Pablo Bay.