San Juan Creek begins in the southern Santa Ana Mountains, a few miles northwest of Lake Elsinore. Its highest elevation is above sea level. Paralleling the Ortega Highway (California State Route 74) the creek flows erratically south, west and occasionally northwest. In the furthest upper reaches of the watershed, the creek is typically ephemeral. The creek channel in the uppermost few miles is a narrow mountain stream with many rapids and waterfalls, which include a series of large cascades, known as San Juan Falls. There are little alluvial deposits in the canyons, and the creek mostly cascades over bedrock. In this upper reach, the pool-and-riffle stream channel structure is evident. There are a few developments within the area, but most of the canyon is too narrow for development, and the only major structure that influences the creek throughout San Juan Canyon is Ortega Highway, which follows the course of the entire canyon.