The Prairies Ecozone provides habitat for many animal species. Intermittent sloughs and ponds on the plains offer major breeding, staging, and nesting grounds for migratory waterfowl using the Central North American flyway. More than half of all North American ducks are born in Prairies Ecozone wetlands. River valleys also offer sheltered habitats important to wildlife, especially during the harsh winters. The Prairies offer unique habitat for the Black-tailed Prairie Dog, while its southern region is home to the Short-horned Lizard and Western Rattlesnake. Manitoba provides habitat for Black Bear, Moose, Sharp-tailed Grouse, Beaver, and Red Fox. Also present are various species of frog and toad. Local fish include Walleye, Lake Whitefish, and Northern Pike.
Considering its area and population, the Prairies Ecozone has a disproportionate number of threatened and endangered wildlife species. At least four vertebrate species -- the Plains Grizzly, Swift Fox, Black-footed Ferret, and Greater Prairie Chicken -- have disappeared from the area. The Peregrine Falcon, Mountain Plover, Eskimo Curlew, Piping Plover, Burrowing Owl, and Whooping Crane are all endangered.
Agriculture has probably had the greatest impact on the ecozone. By replacing natural grasslands with crops, draining wetlands, and destabilizing natural chemical balances in the soil with pesticides, the number and range of wildlife species has changed dramatically. As well, competing, non-native species have been introduced.
Within aquatic ecosystems, high-value fish stocks are under pressure, particularly Walleye and Sauger, which are prized by commercial and recreational fishers. Stocks have been reduced through overfishing and are sensitive to water quality in the controlled-drainage systems as well as to natural fluctuations. For example, contaminants from the widespread use of pesticides have damaged fish habitat.