This dataset contains measurements of CO2, N2O, and diffusive and ebullitive CH4 fluxes from 13 to 24 times along the 24-hour sampling using a high-resolution laser-based Cavity Ring-Down Spectrometer (CRDS PICARRO G2508) coupled to a floating chamber. We performed three 24-hour sampling campaigns in two eutrophic reservoirs (Cubillas and Iznájar) located in southeastern Spain during the stratification period. We measured the GHG fluxes in Cubillas reservoir in 2016 (from July 14th to July 15th) and in 2018 (from June 21st to June 22nd), and in Iznájar reservoir in 2018 (July 8th to July 9th). Hourly measurements of air temperature, surface water temperature, barometric pressure (HANNA HI 9828), and wind speed (MASTECH MS6252A) recorded at the beginning of each flux measurement are also provided.