There have been several recent drinking water incidents in connection with detection of water borne pathogens in Korea. This has led to the need for research to find microorganisms that will indicate the stability of pathogenic removal in water treatment plants (WTPs). We investigated seven microorganisms as potential indicators: four for bacteria [E. coli, fecal coliform (FC), total coliform (TC) and heterotrophic plate counts (HPC)], two for protozoan [aerobic spore formers (ASF) and Clostridium perfringens (CP) spore], and one for viruses (F-specific RNA coliphage). Source water, treated water from each process, and finished water were analyzed periodically from three WTPs, chosen in view of the source water quality and plant size. This study concludes that HPC and ASF appeared to be good indicators of the stability of pathogenic removal. Although this study supports ASF as the best indicating microorganism, the potential use of HPC as an indicating microorganism was demonstrated in this study. From this study, the regrowth problem of HPC in water plants was shown to be negligible depending on the characteristics of the chlorination practice at the WTPs, and temperate climate conditions. The relative importances of each treatment process, for the removal of suggested indicating microorganisms, were found to be as follows: combined process of coagulation and sedimentation with prechlorination > filtration » disinfection, with emphasis on the necessity for the optimization of whole water treatment processes for effective microbial removal.