Human activities have divided the original ecosystems of the Boreal Plains into fragments. As a result, most wildlife populations and their habitats have greatly diminished. Although logging is believed to be partly responsible for an increase in Moose populations since 1955, forest habitat has been lost steadily to timber harvesting. Fish in major rivers and lakes must now face subsistence and commercial fisheries and an array of recreational activities. Within these aquatic ecosystems, there is concern for high-value fish stocks, particularly Walleye and Sauger, which are sought after by both commercial and recreational fishers. Habitats also suffer from increasing water consumption and toxic farm run-off.

Wetlands form an essential part of wildlife habitat, often surviving forest fires to provide refuge and initial browsing lands for wildlife. River levees also provide productive and sheltered areas, especially during harsh winters. Floodplains and associated marshes form unique waterfowl and Muskrat habitat. Bogs, with their ground and tree lichens, are the main habitat for Woodland Caribou.

The most prominent local species include Timber Wolf, Black Bear, Moose, Woodland Caribou, Mule Deer, Elk, and Beaver. Typical bird species are Gray Jay, Common Loon, White-tailed Sparrow, American Redstart, Canada Warbler and Ovenbird. Game birds found in the region include species of grouse, geese, ducks and ptarmigan. The ecozone's lakes and streams teem with Walleye, Lake Whitefish, Northern Pike, Burbot, Perch, and scattered populations of Lake Trout. Little is known of the insects and arthropod communities.

At least four vertebrate species have disappeared from the area: the Plains Grizzly, Swift Fox, Black-footed Ferret, and Greater Prairie Chicken. Peregrine Falcon (anatum), Mountain Plover, Eskimo Curlew, Piping Plover, and Whooping Crane are endangered, according to the Committee on the Status of Endangered Wildlife in Canada. Threatened species include the Borrowing Owl and Ferruginous Hawk.