A 4-month sampling campaign has been conducted for the monitoring of three drinking water treatment plants using flow cytometry and culture-based methods to provide information related to changes in bacterial concentration according to treatments. Flow cytometry is a fast and user-friendly technique enabling bacteria quantification and viability assessment in less than 1 hour. Specific profiles regarding log-reduction of total bacteria were obtained for each treatment plant. Chlorination appeared to be the most effective by causing metabolism inactivation and nucleic acid damages. Ozonation showed a significant impact on cell activity in contrast with ultraviolet treatment which strongly affected bacterial DNA. In addition, the results showed that active bacteria quantified by flow cytometry were significantly correlated with culturable bacteria. This alternative approach appeared as gainful compared to culture methods as it greatly facilitates the diagnosis of treatment plant process for drinking water production monitoring.