While real-time monitoring of physicochemical parameters has widely been incorporated into drinking water treatment systems, real-time microbial monitoring has lagged behind, resulting in the use of surrogate parameters (disinfectant residual, applied dose, concentration x time [CT]) to assess disinfection system performance. Near real-time flow cytometry (NRT-FCM) allows for automated quantification of total and intact microbial cells but has not been widely implemented in full-scale systems. This study sought to investigate the feasibility of NRT-FCM for full-scale drinking water ozone disinfection system performance monitoring. A water treatment plant with high lime solids turbidity in the ozone contactor influent was selected to evaluate the NRT-FCM in challenging conditions. Total and intact cell counts were monitored for 40 days and compared to surrogate parameters (ozone residual, ozone dose, and CT) and grab sample assay results for cellular adenosine triphosphate (cATP), heterotrophic plate counts (HPC), impedance flow cytometry, and 16S rRNA gene sequencing. NRT-FCM provided insight into the dynamics of the full-scale ozone system, including offering early warning of increased contactor effluent cell concentrations, which was not observed using surrogate measures. A strong correlation between log intact cell removal and CT was also not observed (Kendall's tau= -0.09, p=0.04). Positive correlations were observed between intact cell counts and cATP levels (Kendall's tau=0.40, p<0.01), HPC (Kendall's tau=0.20, p<0.01), and impedance flow cytometry results (Kendall's tau=0.30, p<0.01). However, 16S rRNA gene sequencing results showed that passage through the ozone contactor significantly changed the microbial community (p<0.05), supporting the hypothesis that regrowth was occurring in the later chambers of the contactor. This study demonstrates the utility of direct, near real-time microbial analysis for monitoring full-scale disinfection systems.