The Blackfoot River begins in Lewis and Clark County at the Continental Divide, 10 miles (16 km) northeast of the town of Lincoln (4,536 ft; 1,383 m).

It flows westward through the town of Milltown and enters the Clark Fork River approximately five miles (8 km) east of the city of Missoula (3,210 ft; 980 m).

The Blackfoot River is renowned for its recreational opportunities, most notably fly fishing, but also rafting, canoeing, and inner tubing.

The Blackfoot is a fast, cold river with many deep spots, making it prime habitat for several varieties of trout.

The Blackfoot is a Class I river from the Cedar Meadow fishing access site west of Helmville to its confluence with the Clark Fork River for public access for recreational purposes.