The San Luis Rey River rises in two main branches. The mainstem starts east of Rocky Mountain in the Cleveland National Forest and flows generally south-southwest. The West Fork's headwaters rise as a pair of tiny streams, Fry Creek and Iron Springs Creek, just to the north of Palomar Mountain. These two streams combine into the West Fork, which flows southeast through the Mendenhall Valley. The West Fork joins the main stem at Lake Henshaw, a reservoir formed by a dam across the main stem San Luis Rey River.