Flowing through a narrow valley between the Cordillera and coastal range, it has only short tributaries, the principal ones being the Truandó, the Sucio, and the Murrí rivers.

[5] In the 19th and early 20th centuries, the San Juan and the Atrato rivers attracted considerable attention as part of a feasible route for a trans-isthmian canal in Colombia.

[7][8] In 1901, the United States government's Isthmian Canal Commission determined that the Atrato River was not suitable for a canal, due to the length of the route (over 100 miles) and the large amount of silt carried by the river, and recommended Nicaragua and Panama as preferable sites.

[9] In November 2016, the Constitutional Court of Colombia declared the legal personhood of the Atrato River possessing the rights to ‘’protection, conservation, maintenance, and restoration.

As a result, Judge Palacio ruled that the biocultural rights should support the conservation, restoration, and sustainable development of the Atrato River[13] The ruling transpired from the degradation of the river basin from large-scale mining and illegal logging practices, which severely impacted the traditional ways of life for Afro-Colombians and Indigenous people.