Lakes and wetlands, common ecosystems of the high northern latitudes, exchange large amounts of the climate-forcing gases methane (CH4) and carbon dioxide (CO2) with the atmosphere. The magnitudes of these fluxes and the processes driving them are still uncertain, particularly for subarctic and Arctic lakes where direct measurements of CH4 and CO2 emissions are often of low temporal resolution and are rarely sustained throughout the entire year. Using the eddy covariance method, we measured surface-atmosphere exchange of CH4 and CO2 during 2.5 years in a thawed fen and a shallow lake of a subarctic peatland complex. Gas exchange at the fen exhibited the expected seasonality of a subarctic wetland with maximum CH4 emissions and CO2 uptake in summer, as well as low but continuous emissions of CH4 and CO2 throughout the snow-covered winter. The seasonality of lake fluxes differed, with maximum CO2 and CH4 flux rates recorded at spring thaw. During the ice-free seasons, we could identify surface CH4 emissions as mostly ebullition events with a seasonal trend in the magnitude of the release, while a net CO2 flux indicated photosynthetic activity. We found correlations between surface CH4 emissions and surface sediment temperature, as well as between diel CO2 uptake and diel solar input. During spring, the breakdown of thermal stratification following ice thaw triggered the degassing of both CH4 and CO2. This spring burst was observed in 2 consecutive years for both gases, with a large inter-annual variability in the magnitude of the CH4 degassing. On the annual scale, spring emissions converted the lake from a small CO2 sink to a CO2 source: 80% of total annual carbon emissions from the lake were emitted as CO2. The annual total carbon exchange per unit area was highest at the fen, which was an annual sink of carbon with respect to the atmosphere. Continuous respiration during the winter partly counteracted the fen summer sink by accounting for, as both CH4 and CO2, 33% of annual carbon exchange. Our study shows (1) the importance of overturn periods (spring or fall) for the annual CH4 and CO2 emissions of northern lakes, (2) the significance of lakes as atmospheric carbon sources in subarctic landscapes while fens can be a strong carbon sink, and (3) the potential for ecosystem-scale eddy covariance measurements to improve the understanding of short-term processes driving lake-atmosphere exchange of CH4 and CO2.