Abstract Studies of emissions of greenhouse gas (GHG) such as CO2 and CH4 in hydroelectric reservoirs are very important in the debate on whether hydropower can be classified as a ‘clean energy’ source. In this study, GHG emissions in the Topocoro reservoir in Colombia during the first five years after filling were evaluated and related with hydropower generation. The floating static chamber and inverted funnel methodology were used for the collection of GHG and the gas chromatography with flame ionization detector (FID) – methanizer and electron capture detector (ECD) methodology for its detection in the laboratory. The results showed emission values between 256,613 and 654,643 tCO2eq/year. The intensity of gases was also determined in a range between 81 and 148 gCO2eq/kWh, depending on the evolution of the filling and the power generation in the reservoir. The results suggested that as the filling percentage of the surface of the reservoir increases, there will be more GHG emissions, due to the biotic and abiotic decomposition of organic matter. At the same time, higher energy production will be generated.