The objective of this research was to evaluate the degradation and transformation processes of plant material in the hydroelectric reservoirs of Agoyán and Pisayambo that generate greenhouse gases like methane (CH4) and car- bon dioxide (CO2). Field sampling and laboratory analysis were carried out to establish the geographical, and biochemical aspects of the reservoirs, with the aim of establishing the gas flows of interest (methane and carbon dioxide) and determining the correct methodology by applying mathematical models. Reservoir diffusive emissions were measured in situ during field campaigns using a floating chamber, and calculated from gas concentration measurements using the application of an IPCC mathematical model, also the organic matter obtained from the sediment of the reservoirs as a variable, in the same way through a simple modeling by direct estimation using the biochemical oxygen demand (BOD) as a variable was using. The results found in this study indicate that the methane emissions generated in the Agoyán and Pisayambo reservoirs report a maximum value of 3,083.17 tons/year and 7,138.43 tons / year respectively, while CO2 emissions into the atmosphere report values of 136.02 and 239.88 tons / year, indicating that in the Pisayambo reservoir there is more pollution than in the Agoyán reservoir due to emissions of CH4 and CO2.