The most sensitive method of detecting contamination in water supply networks is microbiological testing. Microbiological water safety is evaluated mainly based on the results of traditional tests that rely on bacteria culturing on the so called bacterial growth mediums. Flow cytometry is a modern technology that has been used in microbiology only recently. The diagnostic method based on flow cytometry is much faster and more versatile. Microbiological quality testing was conducted in rzeszowski district, in the area of water network supplied by surface waters, and in the area of water network supplied by underground waters. The scope of the analysis of the microbiological quality of tap water was based on the determination of selected indicators of the sanitary condition of water ie; the total number of psychrophilic and mesophilic bacteria on nutrient agar (reference) called Agar A and additionally called agar supplemented with R, the number of coliforms and faecal streptococci. Determination of the total number of microorganisms by flow cytometry was performed using two dyes SYBR Green and iodide pyridine. Water from underground water intakes, not under the permanent control of microbial had worse microbiological parameters. Used new methods of microbiological assays showed greater amounts of microbiological contamination.