There is little information about the transmission pathways of polyomaviruses. Since many of them are regularly found in urine and feces, the possibility that the waterborne route could transmit these viruses has not been explored. The aim of this study was to evaluate the presence of human polyomaviruses JCPyV, BKPyV, MCPyV, STLPyV and TSPyV along the Belo River (Caxias do Sul-Rio Grande do Sul-RS, Brazil). Four points were investigated, with 13 monthly samplings (March/2015 -March/2016). A total of 52 samples were concentrated by ultracentrifugation, total genomic material was extracted using commercial extraction kit and human polyomaviruses were investigated through real time polymerase chain reaction. A total of 32/52 (61.5%) positive samples were found. Only JCPyV and BKPyV were identified, and they were present in all sampling points. The average viral load of JCPyV was 7E+05 copies/mL and of BKPyV was 5E+04 copies/mL after particle concentration process. Finding such polyomaviruses in this environment suggests contamination through human waste and reinforce the notion that fecal-oral route may represent an important transmission mode for these viruses.(STLPyV). It was detected in human feces by pyrosequencing8, but so far there is no association of STLPyV with diseases.