We quantified the contribution of individual components governing the net ecosystem exchange of CO₂ and how these fluxes respond to environmental changes in a drained and water-saturated site in the polygonal tundra of northeast Siberia. This work finds both sites as a sink for atmospheric CO₂ during the growing season, but sink strengths varied between the sites. Furthermore, it was shown that soil hydrological conditions were one of the key drivers for differing CO₂ fluxes between the sites.