The aim of this study is to assess the synergetic effect of combined ultrasound and ozone treatment on the biological disinfection of water on a large-scale application using viable plate counts and flow cytometry. Escherichia coli B bacteria in saline suspension was treated using a commercially available combined ultrasound and ozone system (USO3 (Ultrasonic Systems Gmbh)) for 16 min. Two analytical methods were used to assess the results in terms of live and dead cells in the bulk liquid: standard viable plate counting recorded in terms of colony forming units per milliliter and flow cytometry. In the latter case 1 mL of bacterial suspension was stained simultaneously with the fluorescent stains SYTO9 and propidium iodide (PI). Transmission electron microscopy was used to generate images identifying the biological effects of different treatments using ultrasound and ozone on bacterial cell walls. Results demonstrated that treatment with ozone alone (1 mg/L) resulted in a significant reduction (93%) in the number of live cells after 16 min treatment whereas ultrasound alone showed only a small reduction (24%). However, a combination of ozone and ultrasound showed a synergistic effect and enhanced the inactivation to 99% after 4 min. A combined ultrasound and ozone treatment of bacterial suspensions using a commercial system affords a promising method for water disinfection that is better than treatment using either method alone. Standard viable plate count analysis is normally used to assess the effectiveness of disinfection treatments; however flow cytometry proved to be a more sensitive method to determine the actual effects in terms of not only live and dead cells but also damaged cells. This type of analysis (cell damage) is difficult if not impossible to achieve using traditional plate counting methodology.