As microbiological parameters are important in monitoring the correct operation of wastewater treatment plants and controlling the microbiological quality of wastewater, the abundances of total bacteria (including intact and damaged bacterial cells) and total viruses in wastewater were investigated using a combination of ultrasonication and flow cytometry. The comparisons between flow cytometry (FCM) and other cultivation-independent methods (adenosine tri-phosphate (ATP) analysis for bacteria enumeration and epifluorescence microscopy (EFM) for virus enumeration) gave very similar patterns of microbial abundance changes, suggesting that FCM is suitable for targeting and obtaining reliable counts for bacteria and viruses in wastewater samples. The main experimental results obtained were: (1) effective removal of total bacteria in wastewater, with a decrease from an average concentration of 1.74 × 10(8)counts ml(-1) in raw wastewater to 3.91 × 10(6)counts ml(-1) in the effluent, (2) compared to influent raw wastewater, the average concentration of total viruses in the treated effluent (3.94 × 10(8)counts ml(-1)) exhibited no obvious changes, (3) the applied FCM approach is a rapid, easy, and convenient tool for understanding the microbial dynamics and monitoring microbiological quality in wastewater treatment processes.