Despite scarce information in the Amazon regions, aquatic environments in tropical mangroves are important carbon deposits, and little is known about the exchange of carbon dioxide (CO2) and methane (CH4) with the atmosphere. We used a dynamic floating chamber to measure CO2 and CH4 fluxes in different aquatic surfaces (river, bore, and stream) on a monthly basis. Water physical-chemical parameters were also measured. Daily tide level variations have influenced CH4 flux in the rainy season. The water surface in the studied Amazonian estuary was a source of CO2 and CH4 to the atmosphere, and the CO2 output was much greater in the rainy season. Their seasonal flux did not present differences among rivers, bore, and streams in the two assessed seasons, but there was monthly variation in their fluxes, which were much higher than in other studies carried out in the tropics (mean production of 3.35 Gg CO2-e y-1).