The eddy-covariance (EC) technique is used to determine mass and energy fluxes between the Earth’s surface and the lower atmosphere at high temporal resolution. Despite the frequent and successful use of the EC technique at terrestrial sites, its application over water surfaces is rare. We present one season of EC measurements conducted on the Rappbode Reservoir, Germany’s largest drinking water reservoir. A floating observation platform in the centre of the reservoir is used for observations of fluxes that were unaffected by surrounding land surfaces and therefore representative of the actual water–atmosphere exchange. The temporal patterns of sensible heat flux are inverted compared to land sites, since the maxima and the minima occur at night and day respectively. The latent heat flux and the evaporation are unexpectedly low for a site where evaporation is not limited by the availability of water. The daily totals in summer and autumn are only 50% and 75% of the potential evaporation assessed by the FAO grass-reference evaporation, respectively. Measurement uncertainties and the effects of the energy balance closure are ruled out as potential factors, so that low values appear to be a general feature of large water surfaces. The observed carbon dioxide fluxes are characterized by distinctive diurnal variations in a typical range for lakes and reservoirs. However, the methane fluxes are low compared to other inland waters.