With water in diminishing supply, desert fish species face great peril. In fact, more than half of the native desert fish species in the Mojave are either federally listed as threatened or endangered or are species of concern. An estimated eight percent are already extinct. Native desert fish often are specifically adapted to the heat and elevated salinity of the water, particularly those species that evolved in small, isolated springs

The Devils Hole pupfish (Cyprinodon diabolis), whose entire population lives in one small spring-fed pool in Nevada, has developed a physiology specifically adapted to the high temperature and salinity of this water. The Ash Meadows National Wildlife Refuge was created in 1984 to preserve the largest concentration of endemic plants and animals in one location in the United States. Twenty-four species, including the Devils Hole pupfish, have adapted to this unique salty desert environment and are found nowhere else in the world. Habitat restoration efforts include converting concrete irrigation ditches back to their natural courses and removing nonnative tamarisk trees and crayfish.

River fish in desert areas are also in decline. For example, native fish of the Colorado River, such as the Colorado squawfish (Ptychocheilus lucius) and razorback sucker (Xyrauchen texanus), have suffered population declines due to dams that have altered the temperature and flow of the river. Introduced sport fish also outcompete these native species.