The diversity of habitats contributes to the diversity of species occurring on the refuge. The open water areas are contain large areas of shallow beds of submergent vegetation. These areas support the large number of molting geese and ducks that can exceed 100,000 birds during late summer and early fall. These aquatic plant beds also support large numbers of warm water and trash fish, which in turn provide food for colonial nesting bird species, and high populations of river otters and mink. The reservoir is habitat for the Utah valvata, an endangered snail. The upland habitats support a variety of shrub-steppe and grassland bird and mammal species. The basalt lava flows provide habitat for some of the more diverse reptile faunas in Idaho. The Idaho dunes tiger beetle, a species of special concern, is found on refuge sand dunes. Several wildlife surveys are performed every year.
Management of wetland areas focuses on providing undisturbed habitat for wildlife. Undisturbed areas are essential for colonial nesting birds, especially American white pelicans, and for molting waterfowl. Undisturbed habitat of this quality and quantity do not occur anywhere else in southeast Idaho. The shallower areas and areas near colonial bird nesting islands are closed to boat traffic. Water levels in the main reservoir are controlled by the Bureau of Reclamation. Levels are raised early in the spring and held stable till late fall so there is no danger of nest flooding. Wildfire control and prevention are important practices; wildfires reduce sagebrush and juniper and favor exotic native grasses, such as cheat grass. Cheatgrass can out-compete native plant species and increase fire frequencies, further degrading the habitat. When and where possible native grasses, forbs, and shrubs are reseeded after wildfires. Integrated pest management is practiced to reduce noxious weeds.