The San Juan River () is a Colombian river that flows into the Pacific Ocean through the Chocó Department. It is approximately and drains a watershed of . The river drains into a large delta that covers nearly . The average discharge of the Rio San Juan is 2,054.67 m<sup>3</sup>/s.
The river begins on Cerro Caramanta in the West Andes. The delta is due north of BahÃÂa Málaga and Buenaventura.
The mouth of the river has extensive stands of mangroves, part of the Esmeraldas-Pacific Colombia mangroves ecoregion.
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<u>Monthly average flow of San Juan River ( mó/second) measured at Penitas station</u><br /><u>Data from 25 years</u>
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A species of snake, Dipsas sanctijoannis, is named after the San Juan River of Colombia, and is native to the watershed.