Quantitative PCR (qPCR) is a convenient tool for monitoring virus concentrations in water and wastewater treatment trains, though it only informs about virus presence, but not infectivity. This limitation can be overcome if the relationship between infectivity loss and genome decay induced by a given disinfectant is known. Here, we performed inactivation experiments using two human enteroviruses, Coxsackievirus B5 and Echovirus 11, with three disinfection methods: low-pressure ultraviolet light ( UV254), free chlorine (FC), and ozone. We compared the inactivation rates as measured by culturing to the decay rates of the whole genome, to evaluate the extent of qPCR-measurable genome damage as a function of inactivation. To determine genome damage, we used an approach that estimates damage across the full viral genome from the measured decay of multiple amplicons distributed across the viral genome. Correlations between inactivation and genome decay were observed for all viruses and all disinfection treatments, but results showed that even among closely related viruses, disinfection methods can damage the viral genome to different extents and that genome damage does not necessarily translate to inactivation. For both viruses, UV254 treatment had the closest relationship between inactivation and genome decay and with ozone, the rate of genome decay exceeded the inactivation rate. Finally, for FC, the ratios between methods were vastly different between viruses. This work provides the basis to relate qPCR measurements to infectivity loss and enables the establishment of molecular monitoring tools for assessing enterovirus inactivation during disinfection treatments of water and wastewater.