<p><strong>Abstract.</strong> Drained peatlands often act as carbon dioxide (CO<sub>2</sub>) hotspots. Raising the groundwater table is expected to reduce their CO<sub>2</sub> contribution to the atmosphere and revitalize their function as carbon (C) sink in the long term. Without strict water management rewetting often results in partial flooding and the formation of spatially heterogeneous, nutrient-rich shallow lakes. Uncertainties remain as to when the intended effect of rewetting is achieved, as this specific ecosystem type has hardly been investigated in terms of greenhouse gas exchange (GHG) exchange. In most cases, methane (CH<sub>4</sub>) emissions increase under anoxic conditions due to a higher water table and in terms of global warming potential (GWP) outperform the shift towards CO<sub>2</sub> uptake, at least in the short-term. Based on eddy covariance measurements we studied the ecosystem–atmosphere exchange of CH<sub>4</sub> and CO<sub>2</sub> (NEE) at a shallow lake situated on a former fen grassland in Northeast (NE) Germany. The lake evolved shortly after flooding, 9 years previous to our investigation period. The ecosystem consists of two main surface types: open water (inhabited by submerged and floating vegetation) and emergent vegetation (particularly including the eulittoral zone of the lake, dominated by <i>Typha latifolia</i>). To determine the individual contribution of the two main surface types to the net CO<sub>2</sub> and CH<sub>4</sub> exchange of the whole lake ecosystem, we combined footprint analysis with CH<sub>4</sub> modelling and NEE partitioning. The CH<sub>4</sub> and CO<sub>2</sub> dynamics were strikingly different between open water and emergent vegetation. Net CH<sub>4</sub> emissions from the open water area were around 4-fold higher than from emergent vegetation stands, accounting for 53 and 13 g CH<sub>4</sub> m<sup>−2</sup> a<sup>−1</sup>, respectively. In addition, both surface types were net CO<sub>2</sub> sources with 158 and 750 g CO<sub>2</sub> m<sup>−2</sup> a<sup>−1</sup>, respectively. Unusual meteorological conditions in terms of a warm and dry summer and a mild winter might have facilitated high respiration rates. In sum, even after 9 years of rewetting the lake ecosystem exhibited a considerable C loss and global warming impact, the latter mainly driven by high CH<sub>4</sub> emissions. We assume the eutrophic conditions in combination with permanent high inundation as major reasons for the unfavourable GHG balance.</p>