It is formed by the confluence of the Atoyaquillo and Colorado Rivers near the village of Santiago Ixtayutla and flows south to its mouth at El Azufre on the Pacific Ocean, on the western border of Lagunas de Chacahua National Park.

[2] Its major tributary is the Atoyac, which drains the Oaxaca Valley and flows into the Río Verde at Paso de la Reina, where a proposal to build a large hydroelectric dam project has been opposed by local communities.

The floodplains of the lower Río Verde valley also began to support large populations and complex society in the Late Formative period (400–100 BC).

[7] In the Postclassic period development shifted away from the floodplains to the city-state of Tututepec, located in the foothills about 16 km east of Río Viejo.

[7] In the context of freshwater fish biogeography, the Verde–Atoyac basin is considered the southern extent of the Nearctic realm on the Pacific coast.