Its furthest tributary, Hell Roaring Creek, originates in the Beaverhead National Forest within a few hundred meters of the North American Continental Divide and Montana-Idaho border near Brower's Spring, at an elevation of about 9,100 feet (2,800 m).

Brower's Spring is near the furthest headwaters of the Missouri River, one of the major watercourses of the central United States.

As such, it is also the furthest headwaters of the entire Missouri-Mississippi river system, today the fourth longest river (after the Nile, Amazon, and Yangtze) on earth and once the third-longest.

It flows west, receiving many tributaries such as Peet Creek and Long Creek, widening into the Lima Reservoir and then passing through a canyon, which ends near Lima, Montana.

From there, it flows northwest through a valley, passing Kidd and Red Rock, and into Clark Canyon Reservoir.