Chlorine disinfection is commonly applied to inactivate pathogenic viruses in drinking water treatment plants. However, the role of water quality in chlorine disinfection of viruses has not been investigated thoughtfully. In this study, we investigated the inactivation efficiency of coxsackievirus B5 (CVB5) by free chlorine using actual water samples collected from four full-scale drinking water treatment plants in Japan under strict turbidity management (less than 0.14 NTU) over a 12-month period. It was found that chlorine disinfection of CVB5 might not be affected by water quality. Japanese turbidity management might play an indirect role in controlling the efficiency of chlorine disinfection.