Microbial populations were studied by plate counts and flow cytometry along the polishing sequence of a wastewater plant. The comparison between plate count and flow cytometry showed comparable trends, but plate counts detected less than 10% of the total intact bacteria counted by flow cytometry. Six months monitoring showed that, in spite of the high ozone doses, the disinfection effect of ozonation was insignificant. This is in agreement with the variability of ozone demand, not only related to chemical oxygen demand or total suspended solids. Membrane-intact bacterial population decreased after ozonation, slightly regrew between ozone and biological activated carbon (BAC), and sharply increased after BAC, probably for damaged bacteria regrowth and saprophytes release; BAC effluent had the highest bacterial counts. Preliminary investigations on the effluent microbial composition showed that the beta Proteobacteria subclass is the most represented in the BAC effluent, whereas the alpha subclass is the most sensitive to ozone effect.