Agusan del Sur is subdivided into 13 municipalities and 1 city. Bayugan City, Bunawan, Esperanza, La Paz, Loreto, Prosperidad, Rosario, San Francisco, San Luis, Santa Josefa, Sibagat, Talacogon, Trento, & Veruela.
Agusan del Sur is an elongated basin formation with mountain ranges in the eastern and western sides forming a valley, which occupies the central longitudinal section of the land. The Agusan River, which flows from Compostela Valley in the south towards Agusan del Norte in the north, runs almost in the middle of the valley and empties at Butuan Bay. The river has twelve tributaries: Wawa, Gibong and Simulao Rivers in the eastern side and Ojot, Pusilao, Kasilayan, Libang, Maasam, Adgawan, Cawayan, Umayam and Ihaon Rivers in the western side. These tributaries are fed by streams and creeks. The southern half of the province from the municipality of Veruela is an area filled with swamps and lakes, the biggest of which is Talacogon Lake.