The Flathead River rises in forks in the Rocky Mountains of northwestern Montana.

The Flathead River, in the northwestern part of the U.S. state of Montana, originates in the Canadian Rockies to the north of Glacier National Park and flows southwest into Flathead Lake, then after a journey of 158 miles (254 km), empties into the Clark Fork. The river is part of the Columbia River drainage basin, as the Clark Fork is a tributary of the Pend Oreille River, a Columbia River tributary. With a drainage basin extending over 8,795 square miles (22,780 km2) and an average discharge of 11,380 cubic feet per second (322 m3/s), the Flathead is the largest tributary of the Clark Fork and constitutes over half of its flow.

The Flathead River is a Class I river in Montana for purposes of recreational access.