The development of increasingly efficient analytical methods is indispensable to ensure a high standard of water quality and to react rapidly against crisis situations. Molecular detection methods have many advantages in comparison with the traditional detection methods. They are more sensitive and specific and they allow a decreased time of analysis. The goal of this paper is to show the benefit of the use of molecular methods for the detection of waterborne bacteria based on the experience in our laboratory. This benefit will be demonstrated based on two examples: the use of PCR for the detection of pathogenic bacteria in karstic areas; and, the use of DVC-FISH for the detection of E. coli in river and drinking water samples. Includes 2 references, tables, figures.