Freshwater reservoirs emit greenhouse gases (GHGs, CO₂ and CH₄) to the atmosphere; however, the sources underlying these emissions are numerous, and their magnitude is not well known. This study quantifies surface CO₂ and CH₄ emissions and all their potential sources in a tropical reservoir. Results highlight the changes in GHG sources along the river–reservoir continuum, with internal metabolism being a key component but highly uncertain and challenging to estimate at an ecosystem scale.