Wikwemikong is located on the northern extremity of the paleozoic Michigan sedimentary basin which is a circular basin structure extending to Chicago in the southwest and Detroit in the southeast. Within the Amabel formation at the Thomas Bay Inlet, along the southern coastline of the reserve, there exists a mineable dolomite rock deposit. The area is rich in Manitoulin fossils of the Silurian and Ordovician ages. Formation of these periods is completely exposed in textbook sequence. The exposed formations lie parallel to the Granville fault. The area also exposes dolomite.

Topography is featured by high plateau areas with steep cliffs to the north and east which gradually dip into the southeast. The southern part is mostly composed of bedrock (sedimentary limestone). The central area between the plateau areas is more fertile and suitable for growing crops. The northern area has shallow rock soils. The shoreline of the reserve proper is mostly rocky. There are several beaches in the protected bays.

Point Grondine is isolated and accessible only by water or by float aircraft. It is characterized by a rocky shoreline and is considered a wilderness area used mostly by trappers, hunters and fishermen, as well as a navigational passage by all vessels.

There are six satellite communities which surround the main village of Wikwemikong;.these include Rabbit Island, Murray Hill/Cape Smith, Wikwemikongsing, Kaboni, South Bay and Buzwah