Tropical rivers might be strong sources of CO₂ and CH₄ to the atmosphere, although there is an enormous data gap. The origin of CO₂ in lowland tropical rivers is not well characterized and can be from terra firme or from wetlands (flooded forests and aquatic macrophytes). We obtained a large field dataset of CO₂, CH₄ and N₂O in the Congo, the second-largest river in the world, which allows us to quantity the emission of these greenhouse gases to the atmosphere and investigate their origin.