San Diego Bay National Wildlife Refuge is an urban refuge located on San Diego Bay in southern California. The refuge, comprising 316 acres of salt marsh and coastal uplands surrounded by urban development, is a critically important area for wildlife because over 90 percent of the historic wetlands of San Diego Bay have been filled in, drained, or diked.

Sweetwater Marsh provides habitat for four endangered or threatened species, including the light-footed clapper rail. It is also the only place in the United Sates where yerba reuma, a member of the heath family, grows naturally. More than 200 species of birds have been recorded on the refuge.

With 90 to 100% of submerged lands, intertidal mudflats, and salt marshes eliminated in the north and central Bay, the new South Bay unit of the refuge will preserve and restore the remaining wetlands, mudflats and eel grass beds to ensure that the bay's thousands of migrating and resident shorebirds and waterfowl will survive into the next century. The approved refuge boundary is 3,940 acres.

The nature center parking lot is located at the western terminus of E Street. A shuttle bus takes visitors to the nature center.

Least tern and snowy plover recovery actions include nest site preparation, predator control, and monitoring at the D Street fill. Light-footed clapper rail recovery actions include salt marsh maintenance, predator control, and monitoring.