Minidoka National Wildlife Refuge extends 25 miles along both shores of the Snake River, upstream from the Minidoka Dam in south-central Idaho. Over half of the refuge is open water, with small patches of marsh that attract concentrations of up to 100,000 ducks and geese during spring and fall migrations. Colonial nesting birds, river otters, and mink feed upon the large populations of cold- and warmwater fish that flourish in shallow beds of submerged vegetation.

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.

The refuge is an important stopover area in the Pacific Flyway. Concentrations of up to 100,000 ducks and geese have been documented during spring and fall migrations, and close to 500 tundra swans can be seen as they migrate through in the spring. The refuge also serves as a molting area for waterfowl in summer. Of the 28 species of waterfowl that use the refuge, those most commonly seen are the Canada goose, mallard, pintail, redhead, gadwall, and wigeon. Colony-nesting birds on the refuge include the Clark's and western grebe, double-crested cormorant, great blue heron, California gull, snowy egret, cattle egret, black-crowned night-heron, and American white pelican. Bald eagles are regularly observed on the refuge in fall and spring, and peregrine falcons are occasionally seen as they migrate through in fall.

Most of the upland areas are shallow soils underlain by fairly recent basalt lava flows, with an occasional sand dune scattered throughout. This mix of rock, sand, and shallow soil supports a diversity of small mammals, reptiles and invertebrates. The divergence point of the Oregon and California Trails was about a mile south of the refuge boundary and an alternate route of the Oregon Trail crossed the northern part of the refuge.