It descends from several short forks in the Mount Jefferson Wilderness in the high Cascades of eastern Marion County.

The South Fork Breitenbush River begins at creeks flowing from Bays Lake and Russell Lake within Jefferson Park at approximately elevation 6,000 feet (1,800 m) and flows west-northwest, joining with other forks.

It flows west-northwest and connects with a half dozen other forks and creeks then turns west-southwest abeam Bald Butte.

The North and South forks flow west, joining 0.25 miles (400 m) east of the small community of Breitenbush.

During the winter draw down of the reservoir, the original bed of the river is visible in its natural course.