Its name has been ascribed as coming from the Ojibwe word aanapii meaning "when?".

The Ahnapee rises in southern Door County and flows generally southeastwardly into northeastern Kewaunee County, past the village of Forestville, where it is dammed.

Downstream of Forestville the river becomes a freshwater estuary of Lake Michigan and is paralleled by a rail trail called the Ahnapee State Trail.

[2] It joins Lake Michigan at the city of Algoma.

[3] The length of the river from Forestville to Algoma has ten public access points.