With respect to their role in the global carbon cycle, natural peatlands are characterized by their ability to sequester atmospheric carbon. This trait is strongly connected to the water regime of these ecosystems. Large parts of the soil profile in natural peatlands are water-saturated, leading to anoxic conditions and to a diminished decomposition of plant litter. In functioning peatlands, the rate of carbon fixation by plant photosynthesis is larger than the decomposition rate of dead organic material. Over time, the amount of carbon that remains in the soil and is not converted back to carbon dioxide grows. Land use of peatlands often goes along with water level manipulations and thereby with alterations of carbon flux dynamics. In this study, carbon dioxide (CO2) and methane (CH4) flux measurements from a bog site in NW Germany that has been heavily degraded by peat mining are presented. Two contrasting types of management have been implemented at the site: (1) drainage during ongoing peat-harvesting on one half of the central bog area and (2) rewetting on the other half that had been taken out of use shortly before measurements commenced. The submitted two-year data set was collected with an eddy covariance (EC) system set up on a central railroad dam that divides the two halves of the (former) peat harvesting area. The data set contains the relative contributions of the surface classes "drained", "rewetted" and "vegetated" to the EC footprint.