About half of the refuge's acreage is open water and wetlands. In this arid landscapet, these resources serve as an oasis drawing numerous wildlife species from miles around. Many species use the bulrush and cattail habitat that lines the lake's small bays. Others use the willows, cottonwoods, and other trees growing near shorelines. The rest of the refuge is low, rolling uplands covered by sagebrush, grasses, and isolated juniper patches among scattered outcrops of basalt.

The climate is semi-arid with about 11 inches of precipitation per year, much of it falling as snow during the winer. Summers are hot and dry with highly variable rain during thunderstorms. Winters are generally modrate but windy. The elevation is about 4,200 feet.

Undisturbed habitats are critical to colonial nesting birds, especially American white pelican, and molting waterfowl. Nowhere else in southeastern Idaho can such habitat be found in this quantity or quality. The refuge uplands are a mix of rock, sand, and shallow soil habitat that supports a diversity of small mammals, reptiles, and invertebrates. The basalt lava flows provide habitat for some of the more diverse reptile fauna in Idaho.

The Idaho dunes tiger beetle, a species of special concern, is found on refuge sand dunes, while the Utah valvata, an endangered snail, inhabits the reservoir. Both sage and sharptailed grouse occupy refuge habitat that is becoming increasingly important in the face of petitions to list these species.

More than 100 years ago, settlers on the Oregon Trail passed just south of the refuge; some crossed on an alternate route through the refuge. Today, thousands of visitors come to Lake Walcott State Park, located within the boundary of Minidoka Refuge, to camp, picnic, hike, observe wildlife, hunt waterfowl, boat, and fish. Sensitive wildlife areas are closed to recreational use.

From Interstate 86: Take exit 21, Cold Water, and follow the gravel road on the north side of the interstate to the refuge gate; or take exit 15, Raft River, then follow the signs on the north side of the interstate to the Gifford Springs boat ramp. Another route to the refuge can be found on the south side of the reservoir from Old Highway 30.

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.