The effects of supercritical CO 2 bubbling (SC-CO 2 ) treatment on the inactivation of microorganisms in water prior to treatment at a municipal water filtering plant (untreated water) were investigated as a way to produce safe drinking water. The coliform bacterial count decreased concomitantly with increasing CO 2 /sample flow rate in the SC-CO 2 treatment. In particular, coliform bacteria could not be detected at a CO 2 /sample flow rate greater than 55%. Also, the total bacterial count dropped rapidly at first stage and slowly at second stage in the SC-CO 2 treatment. Upon observation of Escherichia coli before and after the SC-CO 2 treatment with scanning electron microscopy and transmission electron microscopy, it was observed that the cells treated with SC-CO 2 were shorter than untreated cells and that cytoplasm with low electronic density in the treated cells disappeared. In addition, four types of metabolic enzyme in E. coli cells were effectively inactivated by the SC-CO 2 treatment. These results suggested that SC-CO 2 treatment could effectively inactivate microorganisms in untreated water, and induce morphological changes and inactivate metabolic enzymes of E. coli cells.