The hunting ranges surrounding the Missouri headwaters were coveted and often fought over by Native Americans. Bannock, Blackfeet, Crow, Flathead, and Shoshone all considered it sacred hunting ground. As the Blackfeet gained control of the northern plains, they drove other tribes out of the Missouri headwaters area. The Shoshone moved south and west, the Crow tended to stay off to the east, and the Flathead crossed over from the Bitterroot Valley less often.

Lewis and Clark arrived at present-day Three Forks in July 1805 and declared it the headwaters of the Missouri. Clark and his party returned to the forks on their way back east; from the headwaters they traveled up the Gallatin, crossed Bozeman Pass at Sacagawea’s suggestion, and reached the Yellowstone River near the site of present-day Livingston. They floated the Yellowstone to its confluence with the Missouri, where they were joined by Lewis and his men.

Fur-bearing animals quickly caught the eyes of white trappers and mountain men. Miners made some forays into the mountains, but homesteaders and ranchers were ultimately more successful. Tourism, spurred on by dude ranches and fly-fishers, is now evident in most towns.