Human pathogens in the water are heterotrophic organisms, they consume organic matter as an energy source. Organic carbon, nitrogen and phosphorus in the water often act as limiting factors for bacterial growth and the changes in the microorganism count can be considered as an indication of poor water quality. Microorganism growth potential shows if water parameters influence bacterial growth in number. Positive values of microorganism growth potential show, that water chemical composition and current physical condition of water support the growth of microorganisms. This concept is also connected with biological stability of water and AOC (assimilable organic carbon) method [15]. The presented method was modified in order to make water microbiological analyses more rapid, easier and much more precise. The method of flow cytometry is presented in this study as an alternative, which can be used to determine cell concentration in water samples from the water supply system and also determine the microorganism growth potential. The aim of this study was to determine microorganism growth potential in drinking water samples using flow cytometer.