The park has 250 modern sites divided among two campgrounds. The Lakeshore Campground is situated along Big Stone Bay in a semi-open area and among the 150 sites is a row right off the beach. Pines Campground is across Wilderness Park Drive and has 100 sites, most of them with paved pads and situated in a grove of mature pines. Both campgrounds tend to be filled weekends from early July to mid-August but usually have sites available midweek throughout the summer. The exception is the last week of August through Labor Day when the park is filled daily due to the Mackinac Bridge Walk.

Wilderness also has six rustic cabins scattered throughout the park with three of the trailside cabins situated on the Straits of Mackinac and a short walk from Wilderness Park Drive. Cap's Cabin and Waugoshance Cabin sleep eight each, while Station Point Cabin, an old log structure with wooden floors, has four bunks. Sturgeon Cabin, a short walk from the end of Sturgeon Bay Road, and Nebo Cabin sleep five. All cabins are well used and should be reserved far in advance.

The day-use area is located just east of the campgrounds on Big Stone Bay and includes tables, vault toilets and a wide stretch of sandy beach. The park also has an improved boat launch located just west of Lakeshore Campground.