Inactivation kinetics of autochthonous bacteria during ozonation of wastewater effluents were investigated using cultivation-independent flow cytometry (FCM) with total cell count (TCC) and intact cell count (ICC) and intracellular adenosine triphosphate (ATP) analysis. The principles of the methods including ozone inactivation kinetics were demonstrated with laboratory-cultured Escherichia coli spiked into filtered and sterilized wastewater effluent. Both intracellular ATP and ICC decreased with increasing ozone doses, with ICC being the more conservative parameter. The log-inactivation levels ( log(N/N-0) of E. coli reached the method detection limits for FCM (similar to 3) and ATP (similar to 1.7) at specific ozone doses of >= 0.5 gO(3)/gDOC. During ozonation of four real wastewater effluents, the log-inactivation of autochthonous bacteria with FCM ICC was 0.3-1.0 for 0.25 gO(3)/gDOC and increased to 1.1-2.1 for 0.5 gO(3)/gDOC, but remained at a similar level of 1.5-2.8 for a further increase of the specific ozone doses to 1.0 and 1.5 gO(3)/gDOC. The FCM data also showed that autochthonous bacteria were composed of communities with high and low ozone reactivity. The inactivation levels measured with intracellular ATP were reasonably correlated to ICC (r(2) = 0.8). Overall, FCM and ATP measurements were demonstrated to be useful tools to monitor the inactivation of autochthonous bacteria during ozonation of municipal wastewater effluents. (C) 2016 Elsevier Ltd. All rights reserved.