The river properly begins at the confluence of two tributaries, North Fork Flathead River and Middle Fork Flathead River. Downriver of the forks confluence the third fork joins, the South Fork Flathead River. The North Fork is the longest of the three and is sometimes considered part of the main Flathead River.
The river is part of the Columbia River basin, being a tributary of Clark Fork, which is tributary to Pend Oreille Lake and the Pend Oreille River, which is tributary to the Columbia River.
Portions of the three forks of the Flathead River, South, Middle, and North, are designated National Wild and Scenic River.
In Montana the river continues to flow south, between the Whitefish Range and Salish Mountains to the west and, to the east, the Livingston Range, Lewis Range, Flathead Range, Swan Range. The North Fork Flathead River collects tributaries including Kintla Creek, Whale Creek, Bowman Creek, Quartz Creek, Coal Creek, Camas Creek, and Big Creek, before joining the Middle Fork Flathead River, near Coram, Montana, to form the Flathead River proper.
The North Fork Flathead River in Montana is designated a National Wild and Scenic River. The river is not afforded any protection in British Columbia. This has been the subject of thirty-years of dispute between the United States and Canada. In 1988 the International Joint Commission, ruled that a proposed open pit coal mine would violate the 1909 Boundary Waters Treaty.
Energy development continues to threatened the North Fork, which was deemed the 'wildest river in the contintential United States' by the New York Times in 2004. On February 21, 2008 BP announced to drop plans to obtain drilling rights for coalbed methane extraction in the river's headwaters. However, the Cline Mining Corporation still intends to start a mountaintop-removal coal mining project.
The Middle Fork Flathead River originates in Flathead County, Montana with several headwater streams draining the western side of the Continental Divide. It flows generally northwest, collecting tributaries including Ole Creek, Nyack Creek, and McDonald Creek, before joining the North Fork Flathead River, near West Glacier, Montana, forming the Flathead River proper.
Much of the Middle Fork is designated a National Wild and Scenic River. It drains parts of the Bob Marshall Wilderness and the Great Bear Wilderness of Flathead National Forest. Its lower reach borders on the southern edge of Glacier National Park.
Hungry Horse Dam impounds the lower portion of the South Fork in a reservoir called Hungry Horse Reservoir. A few miles below the dam, the South Fork empties into the main Flathead River, near Hungry Horse, Montana.
A few miles south of Kalispell, the Flathead River empties into the north end of Flathead Lake. Tributaries that flow into the lake include the Swan River.
The Flathead River exits the south end of the lake, near Polson, Montana. Within a few miles the river is impounded by Kerr Dam. Although a natural lake, Flathead Lake is used as a reservoir and its capacity and water releases are controlled by Kerr Dam.
Below the dam, the Flathead River flows generally south, through the Flathead Indian Reservation, collecting tributaries including the Little Bitterroot River, Crow Creek, Mission Creek, and Jocko River. This section of the river flows between the Salish Mountains on the west and the Mission Mountains on the east.
Below the Jocko River confluence, the Flathead River turns west, flowing through the Salish Mountains to join the Clark Fork river near Paradise, Montana.