Coachella Valley Refuge contains the majority of critical habitat within the Coachella Valley Preserve for the Coachella Valley fringe-toed lizard (Uma inornata). This threatened species is restricted to the refuge dune system and a few other small areas.

The refuge also provides for the only significant acreage that is not subject to multiple uses from the recreating public; however, this system is in jeopardy as development threatens sand sources and their travel corridors.

Coachella Valley Refuge is almost entirely closed to the public to protect the Coachella Valley Federally-listed threatened fringe-toed lizard. However, there is a trail that runs through a section of the refuge available for horseback riders.