Natural waters contain organic substances that have a major impact on the quality of water, in particular on its organoleptic properties. They can also change its physical and chemical properties and have a negative impact on the technological processes used during water treatment. There is no doubt that organic substances contained in natural waters have to be removed during treatment processes in order to achieve concentrations consistent with the requirements concerning the quality of water intended for human consumption. A very effective method of organic compounds elimination from water is to use of biologically active filters (BAF). This article presents the results of pilot scale research on the effectiveness of removal of organic compounds from water using filtration through a bed of activated carbon filters, during their technological start-up. The obtained results showed high, more than 91% efficiency of reducing the content of organic compounds expressed by TOC, COD (KMnO4) and UV254 absorbance. The predominant process at the start of the use of carbon filters has been sorption. During the research, the development of biofilm in the filter bed was also controlled. The identification of microorganisms showed the presence of Gram-negative bacteria in the beds of both filter columns.