In Colombia, hydropower share was 70 % of the total installed capacity and more than 50 % of the monthly generation share in 2015, which coincided with the strongest El Niño Southern Oscillation (ENSO) phenomenon reported in the region. ENSO has been recognized as an influential climate pattern on meteorological variables. The generation via hydropower implies the construction of dams and water reservoirs; these flooded areas generate an important amount of Green House Gases (GHG). In this regard, the main aim of this research was to quantify the diffusing emissions of CO2 and CH4 in the flooded areas of the main hydroelectric power generation facilities in Colombia. GHG emissions were calculated by the implementation of an IPCC methodology. The obtained results show that more than 1,042,500 t CO2-Eq (i.e. CO2 and CH4) are emitted in Colombia per year from this source, representing 4.4 % of the total GHG emissions in the country. As the second aim, the vulnerability of Colombia’s energy independence, in terms of power supply to ENSO and climate change was analyzed using the MERRA-2 dataset from NASA, for the years between 2010 and 2017.