Abstract. With increasing air temperatures and changing precipitation patterns forecast for the Arctic over the coming decades, the thawing of ice-rich permafrost is expected to increasingly alter hydrological conditions by creating mosaics of wetter and drier areas. The objective of this study is to investigate how 10 years of lowered water table depths of wet floodplain ecosystems would affect CO2 fluxes measured using a closed chamber system, focusing on the role of long-term changes in soil thermal characteristics and vegetation community structure. Drainage diminishes the heat capacity and thermal conductivity of organic soil, leading to warmer soil temperatures in shallow layers during the daytime and colder soil temperatures in deeper layers, resulting in a reduction in thaw depths. These soil temperature changes can intensify growing-season heterotrophic respiration by up to 95 %. With decreased autotrophic respiration due to reduced gross primary production under these dry conditions, the differences in ecosystem respiration rates in the present study were 25 %. We also found that a decade-long drainage installation significantly increased shrub abundance, while decreasing Eriophorum angustifolium abundance resulted in Carex sp. dominance. These two changes had opposing influences on gross primary production during the growing season: while the increased abundance of shrubs slightly increased gross primary production, the replacement of E. angustifolium by Carex sp. significantly decreased it. With the effects of ecosystem respiration and gross primary production combined, net CO2 uptake rates varied between the two years, which can be attributed to Carex-dominated plots' sensitivity to climate. However, underlying processes showed consistent patterns: 10 years of drainage increased soil temperatures in shallow layers and replaced E. angustifolium by Carex sp., which increased CO2 emission and reduced CO2 uptake rates. During the non-growing season, drainage resulted in 4 times more CO2 emissions, with high sporadic fluxes; these fluxes were induced by soil temperatures, E. angustifolium abundance, and air pressure.