The Agusan River basin is divided into three sub-basins on the basis of topographic features: the upper Agusan River basin, the middle Agusan River basin, and the lower Agusan River basin. The upper Agusan River basin is the section from its headwaters in the mountains of Davao de Oro to Santa Josefa, Agusan del Sur to Veruela, Agusan del Sur, the middle Agusan River basin is the section of the river from Santa Josefa to Amparo, Agusan del Sur while the lower Agusan River basin is from Amparo to its mouth at Butuan.