The manipulation treatment consisted of draining, controlling, and flooding treated sections by adjusting standing water. Inundation increased CH4 emission by a factor of 4.3 compared to non-flooded sections. This may be due to the decomposition of organic matter under a limited oxygen environment by saturated standing water. On the other hand, CO2 emission in the dry section was 3.9-fold higher than in others. CH4 emission tends to increase with deeper thaw depth, which strongly depends on the water table; however, CO2 emission is not related to thaw depth. Quotients of global warming potential (GWPCO2) (dry/control) and GWPCH4 (wet/control) increased by 464 and 148 %, respectively, and GWPCH4 (dry/control) declined by 66 %. This suggests that CO2 emission in a drained section is enhanced by soil and ecosystem respiration, and CH4 emission in a flooded area is likely stimulated under an anoxic environment by inundated standing water. The findings of this manipulation experiment during the autumn period demonstrate the different production processes of CO2 and CH4, as well as different global warming potentials, coupled with change in thaw depth. Thus the outcomes imply that the expansion of tundra lakes leads the enhancement of CH4 release, and the disappearance of the lakes causes the stimulated CO2 production in response to the Arctic climate change.This research was conducted under the JAMSTEC-IARC Collaboration Study with funding provided by the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) under a grant to the International Arctic Research Center (IARC)