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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.