Carbon emissions to the atmosphere from inland waters are globally significant and mainly occur at tropical latitudes. However, processes controlling the intensity of CO2 and CH4 emissions from tropical inland waters remain poorly understood. Here, we report a data-set of concurrent measurements of the partial pressure of CO2 (pCO2) and dissolved CH4 concentrations in the Amazon (n = 136) and the Congo (n = 280) Rivers. The pCO2 values in the Amazon mainstem were significantly higher than in the Congo, contrasting with CH4 concentrations that were higher in the Congo than in the Amazon. Large-scale patterns in pCO2 across different lowland tropical basins can be apprehended with a relatively simple statistical model related to the extent of wetlands within the basin, showing that, in addition to non-flooded vegetation, wetlands also contribute to CO2 in river channels. On the other hand, dynamics of dissolved CH4 in river channels are less straightforward to predict, and are related to the way hydrology modulates the connectivity between wetlands and river channels.