Management of habitat for the Antioch Dunes evening primrose, the Contra Costa wallflower, and the host plant for the Lange's metalmark butterfly is labor intensive. In areas where sand was mined down to the clay substrate, the refuge has imported and reconstructed sand dunes.

Seeds collected from the plants are grown in a nursery for replanting on the refuge. A combination of prescribed burning, mowing, dune reconstruction, hand-weeding, and herbicides are being employed to remove exotic vegetation and improve the substrate for native seedling establishment.

Surveys of all three species, plus other species of special concern, are conducted annually. Applied management research is being conducted in order to develop a comprehensive plan for managing sand dune habitat on the refuge over time.

Fence maintenance and law enforcement are conducted to protect the resources from disturbance and uncontrolled fires.