The article describes the research on the removal of organic matter from natural underground water using biofiltration process. The study was carried out in semi-technical scale on a model filter composed of activated carbon WD-extra. The development of biological activity in a biosorption bed, as well as observations on the relationship between the processes of sorption and biodegradation was evaluated based on the Eberhardt, Madsen, Sontheimer (EMS) test. Leading operation control parameters of biologically active carbon filter BAF included: change of TOC content, dissolved oxygen and permanganate index. To evaluate the colonization of granular carbon determination of ATP value was used. The presence of the biofilm was found by observation using light and scanning microscopes. The organic compounds in the water taken were adsorbed 100% and 70% biodegradable. The combination of sorption process with biodegradation until depletion of activated carbon adsorption capacity allowed in the initial phase of coalbed work for the removal of organic matter in approx. 100% . Formation of biofilm at the right time allowed to extend the filtration cycle and helped lower the TOC by 70%, i.e. from 10 mg C/l to 3-4 mg C/l.