Immediately before the Quaternary Ice Age , the Missouri River was likely split into three segments : an upper portion that drained northwards into Hudson Bay , and middle and lower sections that flowed eastward down the regional slope . As the Earth plunged into the Ice Age , a pre @-@ Illinoian ( or possibly the Illinoian ) glaciation diverted the Missouri River southeastwards towards its present confluence with the Mississippi and caused it to integrate into a single river system that cut across the regional slope . In western Montana , the Missouri River is thought to have once flowed north then east around the Bear Paw Mountains . Sapphires are found in some spots along the river in western Montana . Advances of the continental ice sheets diverted the river and its tributaries , causing them to pool up into large temporary lakes such as Glacial Lakes Great Falls , Musselshell and others . As the lakes rose , the water in them often spilled across adjacent local drainage divides , creating now @-@ abandoned channels and coulees including the Shonkin Sag , 100 miles ( 160 km ) long . When the glaciers retreated , the Missouri flowed in a new course along the south side of the Bearpaws , and the lower part of the Milk River tributary took over the original main channel .