Determination of the microbiological quality of water is one of the central tasks of environmental engineering. Reliability and accuracy of the results depends largely on the sampling system and the methodology carried signs. Typically, they are used traditional indirect methods, breeding: plate method or test tube fermentation. In the methods, seed stocks, it is assumed that each individual cell of bacteria transferred to a solid substrate colony grows. Thus, in fact, the result of the study determines the number of units capable of forming colonies, which is not equivalent to the amount of the living. Even larger errors are subject to the results of the analysis of test tube fermentation, which can only be the most probable number of bacteria in a given volume. It is therefore only estimating the number of microorganisms. Moreover, indirect methods are extremely time consuming (about 1 -7 days of). Flow cytometry is an analytical technique that allows for the rapid measurement of scattered light and fluorescence signals emitted by cells exposed respectively. Allows for a qualitative and quantitative assessment of the physical and biological properties of the cells in a short time. The article presents the results of research on the amount of bacterial cells in different water: surface, groundwater, rainwater and tap water using flow cytometry and compare this results obtained with traditional methods of reference. The microbial results in all the tested waters by flow cytometry are much higher than the amount of the reported conventional methods.