The main branch of the river rises from wetlands in Springfield Township, Oakland County
, northwest of Pontiac. A series of dams create a number of small lakes west of Pontiac, the last of which is Dawson's Millpond. The river is piped under downtown Pontiac, re-emerging to the east of downtown.
The north branch and the middle branch rise in northern Macomb
County and join the main branch in Charter Township of Clinton, which was named after the river. The main branch flows 83.0 miles (133.6 km) from its headwaters to Lake St. Clair
.The Huron-Clinton Metroparks system preserves land in the watershed as public parks.