Straddling the Pecos River, the Refuge consists of an assortment of water habitats surrounded by a harsh, dry environment. The waters support unique wildlife, such as the Pecos pupfish, Roswell spring snail, green throat darter, and Noel's amphipod, along the more than 80 species of dragonflies.

Native grasslands, sand dunes, brushy bottomlands, and re-rimmed plateaus provide a sharp contrast to the wetland habitats of the Refuge. Roadrunners, scaled quail, and horned lizards are commonly seen in these drier areas.