Peroxymonosulfate (PMS) in combination with Cu(II) was examined to inactivate E. coli and MS2 coliphage in natural water. The combined system (i.e., the Cu(II)/PMS system) caused a synergistic inactivation of E. coli and MS2, in contrast with either Cu(II) or PMS alone. Increasing the concentration of PMS enhanced the inactivation of E. coli and MS2, but after a certain point, it decreased the efficacy of the microbial inactivation. In the Cu(II)/PMS system, adding reactive oxidant scavengers marginally affected the E. coli inactivation, but the inhibitory effects of copper-chelating agents were significant. Fluorescent assays indicated that the Cu(II)/PMS system greatly increased the level of reactive oxidants inside the E. coli cells. The sequential addition of Cu(II) and PMS inactivated more E. coli than did adding the two simultaneously; in particular, the inactivation efficacy was much higher when Cu(II) was added first. The observations from the study collectively showed that the microbial inactivation by the Cu(II)/PMS system could be attributed to the toxicity of Cu(I) as well as the intracellular oxidative stress induced by Cu(III) or radical species.