The generally accepted source of the Yukon River is the Llewellyn Glacier at the southern end of Atlin Lake in British Columbia. Others suggest that the source is Lake Lindeman at the northern end of the Chilkoot Trail.

The Missouri in name officially begins at Missouri Headwaters State Park at 4,045 feet in Montana at the confluence of the Jefferson River and Madison River. The Gallatin River joins the river about 0.6 of a mile downstream as it flows northeast. The Jefferson River originates in southwest Montana near the Continental Divide. The Madison and Gallatin Rivers flow out of northwest Wyoming to meet the Jefferson River.