The present study deals with the investigation of soil organic carbon in two water catchments in Northern Rila, Western Bulgaria. Field research, combined with analysis, provided sufficient data. Six key sites were selected and sampled in order to estimate and compare the amount of organic and inorganic carbon in the topsoil. The applied criteria for the choice of sites included: vegetation cover, predominant soil group, level of anthropogenization and transport accessibility. A total number of 13 samples from both catchments were collected and analyzed in the Central laboratory of the Institute of Soil Science, Agrotechnologies and Plant Protection (ISSAPP) “N. Pushkarov“. The results concern the amount and composition of soil organic matter in different soils – Cambisols (Albic, Humic, Dystric), Fluvisols and Umbrosols. The total carbon content of all samples varies between 1.23 and 9.69%. The amount of organic carbon ranges between 0.45 and 3.73%. The results of the study prove once again that the preservation of natural vegetation and current condition of the soil is of great importance for carbon sequestration and climate change mitigation.