BACKGROUND AND OBJECTIVES Water is considered as the most vital component in the origin of life. Water can be contaminated by various industrial toxic and inorganic pollutants as well as pathogens. Contaminated water is responsible for the transmission of various diseases and is considered the main cause of death of approximately 502,000 people worldwide each year. Viruses cause 10 to 10,000 times more disease risk than bacteria. Human polyomaviruses JCV and BKV are good candidates because they are commonly found in environmental water samples from different geographical regions with relatively high abundance. Polyomaviruses are excreted in urine and can spread through water. MATERIALS AND METHODS This research was conducted on 60 samples of recreational water in Mazandaran province (pool, pond, river, sea). Human polyomaviruses JCV and BKV were isolated by filtration method using filters (0.22 and 0.45). Specific primers were designed for BKV and JCV, and the molecular method of polymerase chain reaction (PCR) were detected. RESULTS AND DISCUSSION Human polyoma virus JCV and BKV in recreational water samples based on 60 analyzed samples, JCV was detected in 23 cases (38.33%), but BKV was not observed. CONCLUSION Due to the high prevalence of viral diseases caused by contaminated water and due to the importance of this issue, which will lead to serious risks if health principles are not followed, the presence of BK and JC virus in recreational waters was investigated.