San Juan River may refer to:

• San Juan Creek, also called the San Juan River, located in Orange County, California
• San Juan Creek (Estrella River tributary) in San Luis Obispo County, California
• San Juan River (Colorado River tributary) in Utah, Colorado, and New Mexico in the United States, a tributary of the Colorado River

• San Juan River (Tamaulipas) in Mexico, states of Nuevo León and Tamaulipas
• San Juan River (Veracruz) in Mexico, state of Veracruz

• San Juan River (Guatemala), a tributary of the Pasión River
• San Juan River (Nicaragua), flows from Lake Nicaragua to the Caribbean Sea
• San Juan River (Vancouver Island), in British Columbia, Canada
• San Juan River (Dominican Republic)

• San Juan River (Argentina)
• San Juan River (Chile)
• San Juan River (Colombia)
• San Juan River (Uruguay)
• San Juan River (Venezuela)

• San Juan River (Metro Manila) in the Philippines, a tributary of the Pasig River
• San Juan River (Calamba) in the Philippines, a tributary of Laguna de Bay

• San Juan River Bridge, Manila, Philippines
• San Juan (disambiguation)