The San Juan Creek Watershed covers 133.9 square miles and includes portions of the cities of Dana Point, Laguna Hills, Laguna Niguel, Mission Viejo, Rancho Santa Margarita, and San Juan Capistrano. Its main tributary, San Juan Creek, originates in the Santa Ana Mountains district of the Cleveland National Forest in the easternmost part of Orange County. The Arroyo Trabuco, Oso Creek, and are smaller tributaries.

A comprehensive watershed management study for the Aliso Creek Watershed has been underway for several years. It is currently in the Feasibility Study phase.