Growing season CH4 fluxes were monitored over a two year period following the start of ecosystem‐scale manipulations of water table position and surface soil temperatures in a moderate rich fen in interior Alaska. The largest CH4 fluxes occurred in plots that received both flooding (raised water table position) and soil warming, while the lowest fluxes occurred in unwarmed plots in the lowered water table treatment. A combination of treatment and soil hydroclimate variables explained more than 70% of the variation in ln‐transformed CH4 fluxes, with mean daily water table position representing the strongest predictor. We used quantitative PCR of the
α‐subunit of mcr operon to explore the influence of soil climate manipulations on methanogen abundances. Methanogen abundances were greatest in warmed plots, and showed a positive relationship with mean daily CH4 fluxes. Our results show that water table manipulations that led to soil inundation (flooding) had a stronger effect on CH4 fluxes than water table drawdown. Seasonal CH4 fluxes increased by 80–300% under the combined wetter and warmer soil climate treatments. Thus, while warming is expected to increase CH4 emissions from Alaskan wetlands, higher water table positions caused by increases in precipitation or disturbances such as permafrost thaw that lead to thermokarst and flooding in wetlands will stimulate CH4 emissions beyond the effects of soil warming alone. Consequently, we argue that modeling the effects of climate change on Alaskan wetland CH4 emissions needs to consider the interactive effects of soil warming and water table position on CH4 production and transport.