The mountain range of the Pireneus creates a well-defined division of watersheds. Flowing toward the east small streams drain into the Corumba River, which then joins the Parnaiba River and the Prata finally meeting the Atlantic Ocean between Uruguay and Argentina. To the west the small streams join the Almas River, the regions main watercourse which bisects Pirenopolis, flowing northwest until it reaches the Tocantins River and eventually joins the Marajo and Amazon Rivers and the Atlantic Ocean to the North.

The Pireneus mountain range holds a large underground aquifer, the source of numerous springs in the region. The Corumba and Almas are the areas main rivers.