The susceptibility of waterborne viruses to disinfection is known to vary between viruses and even between closely related strains, yet the extent of this variation is not known. Here, different enteroviruses (six strains of coxsackievirus B5, two strains of coxsackievirus B4 and one strain of coxackievirus B1) were isolated from wastewater and inactivated by UV254, sunlight, free chlorine (FC), chlorine dioxide (ClO2), and heat. Inactivation kinetics of these isolates were compared with those of laboratory enterovirus strains (CVB5 Faulkner and echovirus 11 Gregory) and MS2 bacteriophage. FC exhibited the greatest (10-fold) variability in inactivation kinetics between different strains, whereas inactivation by UV254 differed only subtly. The variability in inactivation kinetics was greater between serotypes than it was among the seven strains of the CVB5 serotype. MS2 was a conservative surrogate of enterovirus inactivation by UV254, sunlight or heat, but frequently underestimated the disinfection requirements for FC and ClO2. Similarly, laboratory strains did not always reflect the inactivation behavior of the environmental isolates. Overall, there was considerable variability in inactivation kinetics among and within enteroviruses serotypes, as well as between laboratory and environmental isolates. We therefore recommend that future disinfection studies include a variety of serotypes and environmental isolates.