The lakeshore's forests have diverse disturbance histories that, through time, have strongly influenced wildlife habitat. Following logging and associated changes to habitat on the islands, there was an irruption of deer on many of the islands. Populations peaked in the 1940-1950's and were followed with major population declines in the 1960's due to excessive hunting quotas, severe winters, and habitat loss due to succession. Currently deer populations are limited to Basswood, Oak, and, most recently, Sand Islands. There may also be a low population of deer on Stockton and Long Islands and deer may occasionally swim to other islands and occur in low numbers for various lengths of time. There is a wintering deeryard on the mainland portion of the lakeshore. Hunting is allowed within the Lakeshore and a special black-powder season for deer on Oak and Basswood Islands has occurred since 1985.
Following logging and associated habitat changes, beaver became established and colonized all the available watersheds on Stockton and Outer Islands. With time, forests have matured and favorable beaver habitat has been reduced. This, in combination with flooding in the early 1990's that destroyed beaver dams and bear predation on Stockton Island, beaver populations have greatly declined. By 1994, no active beaver lodges were found on Stockton Island and recent surveys indicate that beaver numbers have declined on Outer Island. Like deer, beaver can swim between islands and are occasionally found on other islands.
Other large game species on the islands is the black bear; Stockton and Sand Islands are the only islands with a known reproducing population. Bears have overwintered and may occasionally be seen on a number of other islands. Stockton, Oak and Sand Islands are open to hunting.
Other fur-bearers include the snowshoe hare, red fox, coyote, beaver, otter, mink, fisher and muskrat. Small mammals are an important component of the lakeshore's terrestrial fauna and include: shrews, mice, voles, and red squirrels. Some wildlife species that are very common on the mainland, do not occur on the islands, including chipmunks, skunk and raccoon.