The eddy flux of methane (CH4) was measured over 14 months above a restored wetland in western Denmark. The average annual daily CH4 flux was 30.2 mg m−2 d−1, but the daily emission rates varied considerably over time. Several factors were identified that explained some of this variation. (1) Grazing cattle moving through the source area of the eddy flux mast increased the measured emission rates by one order of magnitude during short time periods. (2) Friction velocity exerted a strong control on the CH4 flux whenever there were water pools on the surface. (3) An exponential response of the daily CH4 flux to soil temperature at 20 cm depth was found for most of the study period, but not for parts of the summer season that coincided with a low water level in the river flowing through the wetland. (4) Additional variations in the CH4 emission rates were related to the spatial heterogeneity of the source area. This area covered not only different plant communities but also a gravel road and a river surface, and it had a microtopography that visibly induced a large spatial variability in the wetness of the top soil. It is shown that the control mechanisms for the methane emission from restored wetlands are more complex than those reported for natural wetlands, since they include both management activities and slow adaptive processes related to changes in vegetation and hydrology. On the basis of eddy fluxes of carbon dioxide measured at the same site it is finally demonstrated that the variability in the CH4 fluxes strongly affects the greenhouse gas sink strength of the restored wetland.