The San Juan River may refer to:

• The San Juan River in Cuba.
• The San Juan River in Veracruz, Mexico
• The San Juan River which drains Lake Nicaragua and forms the border between Nicaragua and Costa Rica.
• The San Juan River in Nuevo León and Tamaulipas, Mexico, a tributary of the Rio Grande.
• The San Juan River in Colorado and Utah in the United States, a tributary of the Colorado.