The quantitative importance of northern lakes in terrestrial carbon budgets is uncertain, as year-round observations of carbon fluxes are rare. We measured CH₄ and CO₂ fluxes from a subarctic lake and nearby fen during 2.5 years with one eddy covariance system. We identified drivers of seasonal variability in lake fluxes and show the importance of winter and spring for annual carbon exchange in both ecosystems. The lake as a source of atmospheric carbon partially compensates the fen carbon sink.