The Bighorn River begins as the Wind River in the Rocky Mountains at Wind River Lake, near Two Ocean Mountain and the summit of Togwotee Pass.

The Bighorn River begins as the Wind River in the Rocky Mountains at Wind River Lake, near Two Ocean Mountain and the summit of Togwotee Pass. The Wind River flows southeast receiving the east fork of the Wind River from the north, and enters the Wind River Basin, flowing past Dubois and Johnstown, to Riverton, where it receives the Little Wind River. The river then changes direction to the northeast and then the north, flowing into Boysen Reservoir, which is formed by Boysen Dam. Below the dam it enters the Wind River Canyon, where the river narrows and forms many rapids. At the end of the canyon the Wind River widens out in an area called the Wedding of the Waters where it becomes the Bighorn River and enters the Bighorn Basin. The Bighorn continues northward, passing through Thermopolis, Worland, and Basin. At Greybull it receives the Greybull River, and about 30 mi (48 km) north of that confluence it enters Bighorn Lake, where it is joined by the Shoshone River. North of the confluence with the Shoshone, the reservoir narrows as the river enters the Bighorn Canyon, where it crosses into Montana. At the end of the canyon, the river passes through Yellowtail Dam and Afterbay Dam. The river turns to the northeast and enters the Great Plains. At Hardin the river is joined by the Little Bighorn River. Approximately 50 mi (80 km) downriver from the Little Bighorn, in Big Horn County, the Bighorn empties into the Yellowstone.