The river rises out of Wide Waters[3] on the southern edge of the Baldwin Luther Swamp[4] in Newkirk Township, Lake County at 43°59′32″N 85°45′58″W / 43.99222°N 85.76611°W / 43.99222; -85.76611 (Baldwin River (source)).

Several tributaries rise in the hills to the east of the swamp, and one stream labeled as the Baldwin River on USGS topographic maps rises in section 23 just southwest of the village of Luther.

The river flows south into Cherry Valley Township then to the southwest into the village of Baldwin, where it is joined by Sanborn Creek.

The stream empties into the Pere Marquette at 43°51′36″N 85°52′20″W / 43.86000°N 85.87222°W / 43.86000; -85.87222 (Sanborn Creek (mouth))[5] and thence into Lake Michigan.

The river is notable in American history as the location of the first introduction of brown trout (Salmo trutta) into U.S. waters when on April 11, 1884 the U.S.