Extraction of viral DNA/RNA from environmental samples as part of the analytical procedure in quantifying waterborne viruses, is of great importance. In this study, two commercially available kits were compared to assess their performance, the MO BIO PowerViral Environmental DNA/RNA Isolation kit and the Qiagen QIAamp Viral RNA Mini kit. A performance assessment of extraction kits for detecting and quantifying six human enteric viruses as the commonest waterborne pathogens and one plant virus as an alternative fecal indicator has been carried out using quantitative PCR (qPCR). Water samples were collected from seven sites in Singapore during March and April 2015. In general, a strong association was observed between two different viral DNA/RNA extraction kits and detection frequency of targets (P = 0.017). The Qiagen kit showed higher extraction efficiency than the MoBio kit. However, in terms of quantification, a significant difference was only observed in the occurrences of NoV GI and PMMoV between two different kits (P < 0.05), although the kits showed similar efficiency removing qPCR inhibitors. The Qiagen kit was preferred for routine water quality monitoring.