The natural area encompasses a portion of a complex of forested dunes and swales. The dunes formed as lake levels receded, beginning approximately 12,000 years ago, depositing a series of low sandy beach ridges, ranging from 0.5 to 3 meters high. Since then, the ridges have become forested and the wet swales that developed between them are now either forested or open wetlands. In Michigan, there are fewer than 50 remaining examples of forested wet swale communities of this quality.
This area supports one of the largest known populations in the world of the federal and state-threatened dwarf lake iris, Michigan’s state wildflower. Thousands of iris shoots, and several other plant species of special concern grow in the area.
Thompson's Harbor Natural Area was legally dedicated in 1979. The estate of Genevieve Gillette, a Michigan resident vital to establishing the Wilderness and Natural Areas Program, aided state acquisition of this property.