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.