Cooling towers are specific heat exchangers that provide perfect conditions for microorganism growth. Currently used disinfection methods involving the use of chlorine, chlorine dioxide, UV, or ozone are effective; however, they have many drawbacks. Silver nanoparticles have become one of the most commonly used nano-materials because of their effective antimicrobial properties and low toxicity to mammalian cells. The purpose of our research was to determine the effectiveness of a biocide containing nano-silver; the size of silver particles on the silica surface did not exceed 20 nm. The biocide (the patent for its recipe is currently pending) was proportioned into water taken from the refrigerating cycle of a cooling tower supplied from surface water intake. In this study five doses of biocide were investigated. Comparison of the effectiveness of doses for both mesophilous and psychrophilic organisms was performed. The toxicity assay substantiated the efficacy of silver nanoparticles, but questioned the reliability of nano-silver biocide because of the aquatic environmental hazard.