The most significant habitat present on this Refuge Unit is coastal salt marsh. This habitat supports an array of invertebrates and juvenile fish, and provides nesting, foraging, and high water refuge for many species of birds.

The predominant native habitats within the South San Diego Bay Unit include shallow subtidal habitat and intertidal mudflats. In addition, the salt ponds provide resting and foraging habitat for a variety of avian species, while the levees around the ponds provide important nesting habitat for seven species of ground nesting seabirds.