The stream rises near Tioga Pass in the Eastern Sierra Nevada, more than above sea level, in the Hoover Wilderness of the Inyo National Forest just outside the eastern boundary of Yosemite National Park. The headwaters of the creek consist of many high-altitude lakes, Saddlebag Lake being the largest, as well as permanent snowfields and the Conness Glacier. It flows southeast to Ellery Lake, a natural lake enlarged by a dam, where it turns east and drops over Ellery Lake Falls into the deep Lee Vining Canyon. From there, it flows eastwards out of the mountains past the small town of Lee Vining. The creek terminates at a small sandy delta on the western shore of Mono Lake.