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 red-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.

Native trees such as willows and cottonwoods are scarce on the landscape these days. Salt Cedar, used to stop erosion, has invaded many areas on the refuge. Refuge staff are using mechanical methods to remove this exotic plant. Replanting willows and cottonwoods are underway.

Water manipulation is another important management tool utilized at Bitter Lake NWR. Impoundments are flooded to provide overwintering ducks and shorebirds with necessary food and habitat. For the most part, manageable refuge lakes are filled to capacity during the fall and winter to provide roosting and feeding areas for migratory waterfowl. Many of the lakes are left low during hot summer months when evaporation is highest. Exposing mudflats during spring, summer, and early fall provides the most important feeding area in the state for abundant shorebirds which absolutely require these shallow areas to forage in. The salt flats exposed during spring and summer also provide an important nesting area for snowy plovers, avocets, and least terns. Wetlands are occasionally flooded for short periods to irrigate vegetation and provide a supply of food available for migratory birds as they arrive in the fall.

Fire management is also important at here. Controlled burns allow Service staff to rejuvenate the vegetation and control some exotic plant species.