Beginning at an elevation of 6,487 feet (1,977 m)[2] in the Northern Bitterroot Range of eastern Shoshone County, it flows generally west through the Saint Joe River Valley and the communities of Avery and Calder.

It then turns northwest, passing through Heyburn State Park before reaching its mouth just north of the Kootenai County line.

[5] Much of the river's route through Heyburn State Park is partially flooded due to raised water levels from the Washington Water Power dam at Post Falls on the Spokane River below Coeur d'Alene Lake.

Rush, sedge, and cattails are common in the river's floodplains, which are also used to grow wild rice.

The upper Saint Joe River is also home to the last self-sustaining population of vulnerable bull trout in the Coeur d'Alene Lake watershed.