The city is situated in the central part of the Medium Tietê Zone, which occupies about , or two-fifths of the total area of the Peripheral Depression. It is bounded by Araquá River ("Araquá" means "hole of the world" in Tupí–Guaraní), which has a general north–south route, and also by the Limoeiro and Das Palmeiras lakes. The region where Águas de São Pedro is located is also part of the watershed of the Piracicaba River. The Piracicaba basin extends over an area of , covering the southeastern state of São Paulo and the southern end of Minas Gerais.