Bowdoin National Wildlife Refuge's primary purpose is to preserve and enhance resting, feeding, and breeding habitat for migratory birds and other wildlife. The Refuge attracts migrating waterfowl and shorebirds by the thousands and provides breeding and nesting habitat for ducks, geese, grassland songbirds, and colonial nesting water birds. The area is equally important to a variety of resident wildlife, including raptors, white-tailed deer, pronghorn antelope, sharp-tailed grouse, and coyotes. Threatened species using the Refuge include the bald eagle and piping plover and on occasion peregrine falcons.
North-central Montana is made up of many depressional wetlands created by glaciers 12,000 years ago. Although geologic history indicates that Lake Bowdoin was once an oxbow of the pre-glacial Missouri River channel, today the Missouri River lies nearly 70 miles (110 km) south of Bowdoin NWR. Major habitat types on the Refuge include saline and freshwater wetlands, native prairie, planted dense nesting cover and shrubs. Refuge wetlands total , with the remaining habitat consisting of uplands.