Variability in greenhouse gas emissions from reservoirs creates uncertainty in global estimates of C emissions from reservoirs. This study examines the temporal and spatial variability in CO2 and CH4 surface water concentrations and diffusive fluxes from an Amazonian reservoir using an original data set combining both a high temporal (1 central site × 22 years) and spatial (44 sites × 1 season) resolution monitoring. The gas concentrations at the central site decreased over time and suggested reduced bioavailability of C in the initial flooded soil but exhibited strong seasonal variation. Not accounting for this variability may result in uncertainties in estimates of annual concentrations (ranging from −68.9% to +260% for CH4 and from −71.5% to +156% for CO2) and thus in estimates of diffusive gas emissions. Gas concentrations and diffusive fluxes exhibited high spatial variability in the reservoir, 24 years after impoundment. In particular, diffusive fluxes were higher in littoral and transitional areas than in open areas, suggesting a large contribution of allochthonous C to current gaseous emissions. Not accounting for this spatial variability in diffusive fluxes may underestimate the total emissions expressed in CO2 equivalents from the whole reservoir by 50.7%. Our study stresses the importance of well‐resolved temporal and spatial monitoring to provide reliable estimated of C emissions and a comprehensive understanding of the processes involved; both of these inputs are needed to support decision‐making for developing energy strategies.