The river is named for the Kootenai tribe that lived and hunted in this part of Montana and adjoining territory in Idaho and Canada. They were settled south of Flathead Lake in 1855 with the Salish on the Flathead Reservation.

They were friendly with neighboring mountain tribes but suffered frequently from the incursions of their bitter enemies the Blackfeet, who came across the Continental Divide from the plains on horse stealing and scalp raising expeditions.

First white men in here were trappers and traders for British fur companies as early as 1809. Placer discoveries were made and mining operations commenced about sixty years later.