The typical method of logging was to clear-cut all marketable timber and leave the discarded slashings on the forest floor.

The wilderness is also a template of natural succession that contrasts with most of the Hiawatha National Forest, which continues to be managed for harvestable pulpwood.

The unit's terrain is dominated by postglacial moraines and sand dunes left behind by the Wisconsin glaciation and modified by the stormy climate that accompanied the glacial meltoff.

Two tree families found in large numbers within the Mackinac Wilderness are aspen and birch, both typical of second-growth forests in the Upper Peninsula of Michigan.

In wet areas near the Carp River, the Northern whitecedar is found, although this tree is severely impacted by browsing by whitetail deer.