Tundra ecosystems are especially sensitive to climate change, which is particularly rapid in high northern latitudes resulting in significant alterations in temperature and soil moisture. Numerous studies have demonstrated that soil drying increases the respiration loss from wet Arctic tundra. And, warming and drying of tundra soils are assumed to increase CO2 emissions from the Arctic. However, in this water table manipulation experiment (i.e., flooding experiment), we show that flooding of wet tundra can also lead to increased CO2 loss. Standing water increased heat conduction into the soil, leading to higher soil temperature, deeper thaw and, surprisingly, to higher CO2 loss in the most anaerobic of the experimental areas. The study site is located in a drained lake basin, and the soils are characterized by wetter conditions than upland tundra. In experimentally flooded areas, high wind speeds (greater than ∼4 m s−1) increased CO2emission rates, sometimes overwhelming the photosynthetic uptake, even during daytime. This suggests that CO2 efflux from C rich soils and surface waters can be limited by surface exchange processes. The comparison of the CO2 and CH4 emission in an anaerobic soil incubation experiment showed that in this ecosystem, CO2 production is an order of magnitude higher than CH4 production. Future increases in surface water ponding, linked to surface subsidence and thermokarst erosion, and concomitant increases in soil warming, can increase net C efflux from these arctic ecosystems.