This work reports on results of bacterio‐plankton characterisation in thaw lakes of the northern part of Western Siberia via measurement the number of various groups of heterotrophic bacteria and the intensity of primary production/respiration in the water column. The eutrophic systems at the beginning of lake formation (permafrost thawing) are being replaced by essentially oligotrophic systems at the final, mature stage of the lake development (khasyrey). The CO2 flux from the lake surface to the atmosphere associated with microbial degradation of organic matter (107 ± 50 t C/km2/y) is at least one order of magnitude higher than the riverine organic carbon flux. The future climate evolution in this region, consisting in rising ground temperature and precipitation increase will bring about further acceleration of dissolved organic matter degradation in the water column and amplification of CO2 release to the atmosphere.