A number of infectious diseases of man can be transmitted by water-borne route, whereas outbreaks of water-borne diseases can lead to significant threat. The primary goal of drinking water treatment is just to protect public health by providing safe water that is free of microbial pathogens. This paper describs the characteristics of pathogens, the risk on public health and the water treatment processes for inactivating these pathogens. Pathogenic microorganisms of importance in water industry mainly are bacteria, virus and protozoa,such as cryptosporidium parvum oocysts and Giardia, etc. In addition to conventional treatment processes, the multiple barrier approaches to inactivate microbial pathogens include ozonation, chlorine dioxide, UV and membrane filtration. An additional treatment is needed to deal with cryptosporidium parvum oocysts if its contamination is serious.