Human enteric viruses and emerging viruses such as severe acute respiratory syndrome coronavirus 2, influenza virus and monkeypox virus, are frequently detected in wastewater. Human enteric viruses are highly persistent in water, but there is limited information available for non-enteric viruses. The present study evaluated the stability of hepatitis A virus (HAV), murine norovirus (MNV), influenza A virus H3N2 (IAV H3N2), human coronavirus (HCoV) 229E, and vaccinia virus (VACV) in reference water (RW), effluent wastewater (EW) and drinking water (DW) under refrigeration and room temperature conditions. The decay of infectious viruses was analyzed using a monophasic decay model, which largely showed that human enteric viruses exhibit remarkable persistence in water samples. MNV infectivity decreased significantly after 14 days in EW at room temperature compared to 84 days under refrigerated conditions, with decay rates of 0.230 log TCID50/day at room temperature and 0.040 log TCID50/day under refrigeration. A gradual decline in HAV infectivity was observed at room temperature, whereas at refrigerated temperature, infectious viruses were recovered even after 98 days. HCoV-229E, IAV H3N2 and VACV were completely inactivated in DW and EW at room temperature between 7 and 21 days, with longer stability observed under refrigeration. The decay of IAV H3N2, HCoV-229E and VACV in EW and DW was also assessed in parallel using RT-qPCR to determine genome persistence and viability PCR to determine intact viral capsid persistence. Overall, our results suggest that viability PCR is not suitable for tracking virus decay in water under real-world environmental conditions.