Based on the eddy covariance method we investigate the ecosystem–atmosphere exchange of CH₄ and CO₂ at a eutrophic shallow lake as a challenging ecosystem often evolving during peatland rewetting. Both open water and emergent vegetation are net emitters of CH₄ and CO₂, but with strikingly different release rates. Even after 9 years of rewetting the lake ecosystem exhibits a considerable carbon loss and global warming impact, the latter mainly driven by high CH₄ emissions from the open waterbody.