Natural lakes and reservoirs are emitters of GHGs in the atmosphere contributing to 31% of the annual CO2 emissions of those from fossil fuel combustion. Measurements of GHGs emissions in reservoirs demonstrate that hydropower may actually not be as “green” as once thought. It is estimated that emissions from reservoirs may be equivalent to 7% of the global warming potential (GWP) of other documented anthropogenic emissions. Aim of this work is to assess the impact of water quality deterioration and the subsequent increment of biological productivity of a waterbody on GHGs emissions. Therefore, the trophic state, the carbonic GHGs emissions and the GWP of one natural lake domestic wastewater receiver and two different age hydroelectric reservoirs, located in North West Greece, were studied. Gross emissions of CO2 and CH4 were in-situ measured using a static floating chamber and specific emissions as well as GWP were calculated. Furthermore, water quality and trophic state were evaluated based on the application of ΥΔΩΡ (hydõr) Water Quality Index and Florida Trophic State Index using physicochemical characteristics measurements. Data statistical interpretation revealed that CH4 has strong positive correlation with GWP, temperature, water quality and trophic state. There is a seasonal variation of GWP that follows the seasonal variation of CH4 emissions induced by water temperature. Specific CH4 emission rate presents the most reliable indicator for assessing the impact of a waterbody in terms of GWP, especially of a hypertrophic one. Water quality and trophic state indices can be used for a rough comparison of GWP between waterbodies with the same climatic conditions.