The river begins in the Bob Marshall Wilderness south of Glacier National Park, as does the Middle Fork Flathead River, at the confluence of two streams, Danaher Creek and Youngs Creek, between the Flathead Range and the Swan Range.

For some 40 miles (64 km), the river flows freely north-northwest, meandering through a forested and undeveloped valley.

Hungry Horse Reservoir occupies much of the lower half of the river, covering 97 square miles (250 km2).

The reservoir trends north then northwest, and the river then passes through the arched Hungry Horse Dam, just a few miles above the mouth.

After it leaves the dam, the river enters a narrow gorge and, exiting the canyon for the final time, runs northwest past the town of Hungry Horse, then joins the Flathead River, just a few miles below its headwaters at the North Fork and Middle Forks' convergence.