Along the coast, glaciers have incised the valley floors below sea level, creating deep, narrow fiords with vertical walls up to 900 m in height. These coastal/marine areas, including the northern fiords of the park, are rich in wildlife. Six species of marine mammals (including the polar bear) have been recorded in the park and an additional seven species found in adjacent waters may use the park as well.

Eight species of terrestrial mammals are found in the park and 28 species of birds breed in the park (with another 11 species suspected to breed in the park). Thirteen species of freshwater and marine fish have also been recorded in the park. Several other species of wildlife found in the greater park ecosystem on the Cumberland Peninsula, and in the waters of Cumberland Sound and Davis Strait adjacent to the park may sometimes occur within park boundaries.

The greater park ecosystem encompasses a large area of relatively pristine wilderness with a high level of ecological integrity. Today, Auyuittuq National Park is virtually indistinguishable from much of its surrounding greater park ecosystem. However, the park protects portions of the habitats required to sustain large animals that transcend boundaries, including caribou, polar bear, wolves and some marine mammals.

Several species that occur in the park are being assessed through the Species at Risk Act process. The polar bear, the Eastern High Arctic / Baffin Bay population of beluga, and the narwhal have been identified by the Committee on the Status on Endangered Wildlife in Canada as species of special concern.