The headwaters of the Merced River are at at the foot of the Clark Range subrange of the Sierra Nevada, rising at the confluence of the Triple Peak Fork and Merced Peak Fork after they cascade down glacially polished slopes from the high country in the southeastern corner of Yosemite National Park. From its headwaters, the river flows north for a short distance and collects the Lyell Peak Fork. The course of the Merced then turns to the north west and flows through a steep walled canyon for where the river receives the Red Peak Fork and then collects into Washburn Lake, above sea level.