Bear Lake Refuge lies in the mountain-ringed Bear Lake Valley in southeastern Idaho, north of the deep body of water that is the namesake of both the valley and the refuge. The refuge encompasses approximately 18,000 acres of the Dingle Swamp, a mosaic of bulrush cattail marsh, open water, and flooded meadows.

Portions of the refuge include scattered grasslands and brush-covered slopes. The habitats on the refuge are managed primarily for waterfowl and water bird production. The refuge's White-Faced Ibis colony of 5,000 birds is one of the largest in the West.

Trumpeter swans are beginning to nest and use the refuge in May, Canada geese hatch by the hundreds, ducks and cranes follow shortly thereafter. All can be viewed throughout the refuge. The refuge also includes the 1,015-acre Thomas Fork Unit near the Wyoming border and Oxford Slough Waterfowl Production Area near Oxford, Idaho.