From its headwaters in southwestern Colombia near the city of Popayán, it joins the Magdalena River near Magangué in Bolívar Department, and the combined river eventually flows out into the Caribbean Sea.

The river is under the supervision of the Cauca Regional Corporation and the Cauca Valley Regional Autonomous Corporation, and is navigable for 640 km (400 mi) above its junction with the Magdalena.

On November 18, 2007, Colombian newspaper El Tiempo reported that the river was receiving an average of 500 tons of residual waste a day.

Pollution from the city of Popayán, seven gold mines that also add industrial pollutants such as mercury, some 8 sand mills, plus a couple of mines of coal and bauxite.

[1] The Hidroituango energy dam project has seriously affected the Cauca River.