It rises out of Hovey Lake at 46°17′36″N 86°42′20″W / 46.29333°N 86.70556°W / 46.29333; -86.70556[3] on Hiawatha National Forest land in Alger County and flows south and east through a lake district and on through Schoolcraft County.

It then flows east and south about 2.5 miles where it merges with the Manistique River, which then flows through Manistique and into Lake Michigan at 45°56′56″N 86°14′45″W / 45.94889°N 86.24583°W / 45.94889; -86.24583.

The Indian River is a National Wild and Scenic River, with 12 miles (19 km) designated "Scenic" and 39 miles (63 km) designated "Recreational".

This river is popular with paddlers although the section from Hovey Lake to Doe Lake is not maintained for canoes or kayaks and requires many portages.

From Doe Lake to Indian Lake is periodically maintained for clear passage by the forest service, but portages may still be required due to the abundance of dead-falls.