Soil organic carbon (SOC) is a basic element which influences soil processes. In peatlands, carbon is stored in various organic compounds, and any alteration of peatland, especially drainage, leads to the changes in SOC pools. The aim of the study was to assess the relations between labile carbon and humus fractions, and state of topsoil transformation as well as the relative composition of labile carbon pool in organic soils affected by drainage and re-wetting. We extracted labile carbon with hot water (HWC) and stable carbon in the form of humus substances (chemical extraction), and measured the amounts on CN analyser. In the labile pool, we estimated the relative amount of hydrophilic and hydrophobic fractions using chromatographic techniques. The state of soil transformation was assessed on the base of water-holding capacity index (W1). Mean HWC concentrations were higher in drained peatlands than in the rewetted one. The chromatographic analysis of labile carbon showed that HWC fraction contained more hydrophilic than hydrophobic organic compounds. High concentration of humus fractions in drained peatlands resulted in the higher humification degree, which amounted to 44.8%. The drainage and soil use influenced the quantities of studied labile and stable carbon pools. The HWC concentration proved to be a good indicator of biological changes in organic soils, and may be a good index to monitor the initiation of peat formation at rewetted peatlands which had been previously drained. The state of transformation expressed by W1 index influenced labile carbon pool and relative amounts of hydrophilic part of HWC, as well as free fulvic acids and stable carbon pool (humification degree). The release of labile organic carbon from peatlands implies a loss of sequestered carbon. The stable carbon pool, when subjected to drainage, becomes vulnerable to microbial changes, and successively becomes secondary humified, therefore the value of humification degree increases.