The San Juan River's headwaters take drainage from the southern slopes of the
Seymour Range. Its largest fork begins at a small unnamed pond in
Cowichan Valley Regional District and forms the primary headstream. From here the San Juan River flows southwest into "Pete's Pond" before continuing its descent south. It then enters the
Capital Regional District before pooling briefly in a large unnamed pond. The river then continues south before meeting its first named tributary, Clapp Creek. From here the river swings west-southwest, growing considerably in size as continues down the valley. The San Juan River then meets its first major tributary, Fleet River. From here the river winds through a canyon before it opens up into a broad valley. It meets the major tributaries of Lens Creek and Harris Creek before meeting an outlet stream of Fairy Lake. From here the San Juan River meanders considerably and breaks off into a pair of major branches, forming a large
estuary. The smaller northern branch meanders west before sharing an outlet to
Port San Juan with the
Gordon River. The larger southern branch meanders southwest and empties into Port San Juan just north of
Port Renfrew. ==Estuary==