Human health and biological safety problems resulting from urban drinking water pipe network biofilms pollution have attracted wide concern. Despite the inclusion of residual chlorine in drinking water distribution systems supplies, the bacterium is a recalcitrant human pathogen capable of forming biofilms on pipe walls and causing health risks. Typical drinking water bacterial biofilms and their response to different concentrations of chlorination was monitored. The results showed that the four bacteria all formed single biofilms susceptible to sodium hypochlorite. After 30 min disinfection, biomass and cultivability decreased with increasing concentration of disinfectant but then increased in high disinfectant doses. PMA-qPCR results indicated that it resulted in little cellular damage. Flow cytometry analysis showed that with increasing doses of disinfectant, the numbers of clusters increased and the sizes of clusters decreased. Under high disinfectant treatment, EPS was depleted by disinfectant and about 0.5–1 mg/L of residual chlorine seemed to be appropriate for drinking water treatment. This research provides an insight into the EPS protection to biofilms. Resistance of biofilms against high levels of chlorine has implications for the delivery of drinking water.