AIMS: Viral outbreaks associated with swimming pools have been described worldwide. The objective of this study was to examine the extent of viral contamination in indoor and outdoor swimming pools. METHODS AND RESULTS: Pools were examined for the presence of human enteric viruses (adenovirus, norovirus and enterovirus) and nonenteric viruses (papillomavirus and polyomavirus—BK, JC, KI, WU and Merkel cell). Bacteriological parameters were also evaluated. The analysed pool waters met microbiological quality standards. Enteric viruses were not detected. On the other hand, papillomaviruses (HPV8, 12, 23, 25, 120 and unclassified HPVs) and polyomaviruses (JC and Merkel cell polyomaviruses) were detected in 9/14 samples (64%). The number of HPV DNA copies in pool waters, measured by quantitative Real‐time PCR, ranged from 1.27E+04 to 1.13E+05/10L. CONCLUSION: Results show that a variety of nonenteric viruses may be discharged in pool waters by various secretions and excretions from infected individuals or asymptomatic carriers. SIGNIFICANCE AND IMPACT OF THE STUDY: To the best of our knowledge, this is the first report on human papillomaviruses and polyomaviruses in swimming pools. The likelihood that these viruses can be transmitted by recreational activities deserves to be explored in future studies.