Abstract As surface temperatures are expected to rise in the future, ice-rich permafrost may thaw, altering soil topography and hydrology and creating a mosaic of wet and dry soil surfaces in the Arctic. Arctic wetlands are large sources of CH 4 , and investigating effects of soil hydrology on CH 4 fluxes is of great importance for predicting ecosystem feedback in response to climate change. In this study, we investigate how a decade-long drying manipulation on an Arctic floodplain influences CH 4 -associated microorganisms, soil thermal regimes, and plant communities. Moreover, we examine how these drainage-induced changes may then modify CH 4 fluxes in the growing and nongrowing seasons. This study shows that drainage substantially lowered the abundance of methanogens along with methanotrophic bacteria, which may have reduced CH 4 cycling. Soil temperatures of the drained areas were lower in deep, anoxic soil layers (below 30 cm), but higher in oxic topsoil layers (0–15 cm) compared to the control wet areas. This pattern of soil temperatures may have reduced the rates of methanogenesis while elevating those of CH 4 oxidation, thereby decreasing net CH 4 fluxes. The abundance of Eriophorum angustifolium , an aerenchymatous plant species, diminished significantly in the drained areas. Due to this decrease, a higher fraction of CH 4 was alternatively emitted to the atmosphere by diffusion, possibly increasing the potential for CH 4 oxidation and leading to a decrease in net CH 4 fluxes compared to a control site. Drainage lowered CH 4 fluxes by a factor of 20 during the growing season, with postdrainage changes in microbial communities, soil temperatures, and plant communities also contributing to this reduction. In contrast, we observed CH 4 emissions increased by 10% in the drained areas during the nongrowing season, although this difference was insignificant given the small magnitudes of fluxes. This study showed that long-term drainage considerably reduced CH 4 fluxes through modified ecosystem properties.