An average of 54,000 ducks and geese use this IBA during migration. In 2003, weekly counts of spring and fall migration totaled 33,230 shorebirds. The Agassiz Pool has the largest Franklin's Gull colony in Minnesota and is one of the largest in North America. The Black Tern breeding population in 2005 was estimated at 2,200. An Eared Grebe colony has had 50 to 500 breeding birds over the past 15 years. Fall populations of migrating Sandhill cranes number between 500 and 1,000. American White Pelicans use the refuge for loafing and number between 3,000 to 5,000.
The refuge has hosted long term research on American and Least Bitterns as well as pioneering research on Franklin's Gulls, Sandhill Cranes and Black Terns. There is a long history of management and ecological research on waterfowl species including brood counts, pair counts, duckling survival and nest predation.
A 4,000 acre wilderness in the north-central part of the refuge contains a black spruce & tamarack bog with many unique plants. Open water and freshwater marshes, willow, woodland, and upland grassland are some of the natural habitats found here.