Tijuana Slough Refuge is located in the most southwestern corner of the contiguous United States. It is one of southern California's largest remaining salt marshes without a road or railroad trestle running through it.

This important salt marsh is surrounded by San Diego County and Tijuana, Mexico, with a population of 4.3 million people. Within this international bioregion, the refuge maintains essential habitats for many migrating shorebirds and waterfowl along the Pacific Flyway.

Tijuana Slough provides critical habitat for the Federally-listed endangered California least tern, light-footed clapper rail, least Bell's vireo, and salt marsh bird's-beak, an endangered plant species. Designated as a Globally Important Bird Area by the American Bird Conservancy, over 370 species of birds have been sighted on the refuge.

The refuge's habitat and wildlife management programs focus on the recovery of endangered species through research, habitat restoration, and environmental education.