Drinking water disinfection provides the final barrier to waterborne transmission of a wide variety of potentially waterborne infectious agents including pathogenic bacteria, viruses, and protozoa. These agents differ greatly in their innate resistance to inactivation by disinfectants, ranging from extremely sensitive bacterial agents to highly resistant protozoan cysts. The close similarity between microorganism inactivation rates and the kinetics of chemical reactions has long been recognized. Ideally, under carefully controlled conditions, microorganism inactivation rates simulate first order chemical reaction rates making it possible to predict the effectiveness of disinfection under specific conditions. In practice, changes in relative resistance and deviations from first order kinetics are caused by a number of factors including microbial growth conditions, aggregation, and association with particulate materials. The net effect of all of these factors is reduction in the effectiveness and predictability of disinfection processes.