The study covers the period of operation of Nuclear Power Station (NPS) Jaslovské Bohunice and the period of construction and trial run of NPS Mochovce, West Slovakia, from July 1996 to November 1998. The incidence of physiological groups of microorganisms indicating contamination and self-purification tendencies in waters (ammonifying, proteolytic, amylolytic, lypolytic, ferric and manganese bacteria) bacterial indicators of general pollution (psychrophiles, mesophiles and spore-forming bacteria) as well as indicators of faecal pollution (enterococci, coliform and thermotolerant coliform bacteria) were monitored in water samples taken from selected localities in the vicinity of both stations monthly or bi-monthly. The analysis of bacterial spectra showed that during the period of last two years, the industrial wastewater outflows neither contributed to the bacterial contamination nor affected negatively the bacterial biotops of primary recipients and waters of Váh and Hron rivers. Within phototrophic microorganisms, cyanobacteria and algae, altogether 708 species and infraspecific taxa were determined. No negative influence of the activities of both NPS on species composition, morphology or physiological properties has been noticed using applied methods of investigations. Complex evaluation of the impact of NPS Jaslovské Bohunice and Mochovce operations on aquatic bacterial biocenosis will require permanent investigation and monitoring.