San Mateo Creek has its source, at an elevation of 2800 feet, in the canyon on the west face of the unofficially named 3,591 ft. San Mateo Peak, at the western end of the ridge running west then northwest from Elsinore Peak to Morrell Canyon, south and west of the Morrell Potrero in the Elsinore Mountains. From its headwaters south of Lake Elsinore inside the Cleveland National Forest, San Mateo Creek runs southwards through the valley of the old Rancho at the Potrero de la Cienaga which as its name suggests feeds the creek with several springs. The canyon widens and deepens until it is roughly in depth. After running south for several miles it turns southeast to the where it tumbles down to its confluence with Los Alamos Canyon Creek, that comes in from the left. This creek with its tributary Wildhorse Canyon Creek and two unnamed arroyos drain the southern slopes of Elsinore Peak. Another unnamed arroyo drains the western Santa Rosa Plateau and the east slope of the Squaw Mountain highland and descends to the north to join the creek where it turns to the west.