The 36,000 acres of upland habitat include native and introduced grasslands, thick woodlands, shrub thickets, and some cropland. The northern portion of the Refuge is primarily river valley with a narrow band of adjacent upland habitat. The southern portion of the Refuge contains about 16,000 acres of native prairie interspersed with aspen and brush-covered sandhills and 4,200 acres of wooded river bottom.

Wetland habitats include deep and shallow marshes within the Souris River flood plain. Five dikes with water control structures have restored 23,000 acres of open water, marsh, and wet meadow habitat for migratory bird production and migration use.

While the primary objective of the Refuge is waterfowl production, the area has a very diverse population of other bird species. More than 250 species have been noted including sharp-tailed grouse on their dancing grounds in the spring; Swainson's hawks in great numbers in the fall; a wide variety of waterbirds including five species of nesting grebes; and relatively rare small birds such as Spragues's pipits, Baird's sparrows, and LeConte's sparrows. The Refuge has been designated as a Globally Significant Bird Area and is a regional site in the Western Hemisphere Shorebird Reserve Network.