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Abstract Permafrost degradation in peatlands is altering vegetation and soil properties and impacting net carbon storage. We studied four adjacent sites in Alaska with varied permafrost regimes, including a black spruce forest on a peat plateau with permafrost, two collapse scar bogs of different ages formed following thermokarst, and a rich fen without permafrost. Measurements included year‐round eddy covariance estimates of net carbon dioxide (CO₂), mid‐April to October methane (CH₄) emissions, and environmental variables. From 2011 to 2022, annual rainfall was above the historical average, snow water equivalent increased, and snow‐season duration shortened due to later snow return. Seasonally thawed active layer depths also increased. During this period, all ecosystems acted as slight annual sources of CO₂(13–59 g C m⁻² year⁻¹) and stronger sources of CH₄(11–14 g CH₄ m⁻²from ~April to October). The interannual variability of net ecosystem exchange was high, approximately ±100 g C m⁻² year⁻¹, or twice what has been previously reported across other boreal sites. Net CO₂release was positively related to increased summer rainfall and winter snow water equivalent and later snow return. Controls over CH₄emissions were related to increased soil moisture and inundation status. The dominant emitter of carbon was the rich fen, which, in addition to being a source of CO₂, was also the largest CH₄emitter. These results suggest that the future carbon‐source strength of boreal lowlands in Interior Alaska may be determined by the area occupied by minerotrophic fens, which are expected to become more abundant as permafrost thaw increases hydrologic connectivity. Since our measurements occur within close proximity of each other (≤1 km²), this study also has implications for the spatial scale and data used in benchmarking carbon cycle models and emphasizes the necessity of long‐term measurements to identify carbon cycle process changes in a warming climate. 

Abstract Rich fens are common boreal ecosystems with distinct hydrology, biogeochemistry and ecology that influence their carbon (C) balance. We present growing season soil chamber methane emission (F_CH4), ecosystem respiration (ER), net ecosystem exchange (NEE) and gross primary production (GPP) fluxes from a 9‐years water table manipulation experiment in an Alaskan rich fen. The study included major flood and drought years, where wetting and drying treatments further modified the severity of droughts. Results support previous findings from peatlands that drought causes reduced magnitude of growing seasonF_CH4,GPPandNEE, thus reducing or reversing their C sink function. Experimentally exacerbated droughts further reduced the capacity for the fen to act as a C sink by causing shifts in vegetation and thus reducing magnitude of maximum growing seasonGPPin subsequent flood years by ~15% compared to control plots. Conversely, water table position had only a weak influence onER, but dominant contribution toERswitched from autotrophic respiration in wet years to heterotrophic in dry years. Droughts did not cause inter‐annual lag effects onERin this rich fen, as has been observed in several nutrient‐poor peatlands. WhileERwas dependent on soil temperatures at 2 cm depth,F_CH4was linked to soil temperatures at 25 cm. Inter‐annual variability of deep soil temperatures was in turn dependent on wetness rather than air temperature, and higherF_CH4in flooded years was thus equally due to increased methane production at depth and decreased methane oxidation near the surface. Short‐term fluctuations in wetness caused significant lag effects onF_CH4, but droughts caused no inter‐annual lag effects onF_CH4. Our results show that frequency and severity of droughts and floods can have characteristic effects on the exchange of greenhouse gases, and emphasize the need to project future hydrological regimes in rich fens.