The Rio Jaboatão flows through eastern Pernambuco, passing through the city of Jaboatão dos Guararapes before emptying into the Atlantic Ocean at coordinates 8°13′31″S 34°55′35″W. The mouth of the river sits on the boundary between the municipalities of Jaboatão dos Guararapes and Cabo de Santo Agostinho. The city itself lies approximately 45 metres above sea level, just west of Recife, placing the river within the greater Recife metropolitan area. The river is positioned roughly halfway between Recife and Porto de Galinhas — less than 30 minutes from Boa Viagem beach and approximately 40 minutes from Porto de Galinhas — making it accessible from either base.

The Pirapama River is a significant tributary of the Jaboatão, and its inflow has a direct effect on water conditions. During periods of heavy or sustained rainfall, the river can become noticeably turbid and discolored. The drier months — roughly September through May — offer more stable and clearer water conditions, making that period the more practical time for water-based activities. The remaining months, corresponding to the wetter season, tend to bring elevated turbidity.

One established access point near the river mouth is the Acqua Mariner marina, located at Rua José de Souza Marmelo, 360, in the Barra de Jangada neighborhood of Jaboatão dos Guararapes. The area carries historical significance as the site of two battles during the 17th-century conflict between Portuguese and Dutch forces in the region.