Inland waters are an import source of greenhouse gases for the atmosphere. In particular, the emissions of methane from lakes and reservoirs are suspected of almost offsetting the terrestrial carbon sink. However, the estimates found in the literature are subject to large uncertainties due to both missing data and methodological limitations. In particular, there is a gap of observations in the temperate climate zone, and data are especially scarce from eutrophic waters despite the fact that the emissions increase with the degree of eutrophication. We present data from a eutrophic reservoir in the temperate climate zone, measured continuously with a floating eddy-covariance system. Data from two seasons are analyzed, both starting and ending with spring and autumn mixing, respectively, and including the complete period of summer stratification. During the spring and summer months, clear diurnal patterns for the carbon dioxide fluxes were detected in the eddy covariance data reflecting the interplay between photosynthesis and respiration. However, this daylight-driven oscillation weakened with the onset of autumn and disappeared at the end. In contrast to the carbon dioxide fluxes, the methane fluxes did not show any daytime dynamics. Notwithstanding, distinct seasonal patterns with increasing CH4 emissions over summer appeared. The carbon dioxide balance was about −9.8 and −71.0 g C m⁻², in the first and second season, respectively. Thus, based on the eddy covariance measurements, the reservoir was a carbon dioxide sink in both study periods. However, the difference between the two seasons indicates a distinct inter-annual variability. The seasonal methane emissions were 24.0 g C m⁻² and 23.2 g C m⁻², respectively. Accordingly, the seasonal carbon budget resulted in 15.1 g C m⁻² and −47.8 g C m⁻², respectively, meaning the reservoir was a carbon source in the first and a sink in the second study period. However, considering the significant higher warming potential of methane and transposing these emissions into carbon dioxide equivalents, the reservoir contributed to the greenhouse potential of the atmosphere in both study periods.