Secondary disinfection provides an essential residual that prevents the regrowth of microorganisms in the distribution network. Chlorine, chloramines, and chlorine dioxide are commonly used as secondary disinfectants. However, chloramine is the most commonly used secondary disinfectant. Chloramine is not virucidal and is only slightly effective in killing Giardia cysts.

When water passes through various stages of purification, it must be disinfected to the extent necessary, depending on its intended use. For example, drinking water, after purification and removal of suspended and dissolved substances, must be free from any microbial contamination and not pose any health and safety risk to the consumer. The destruction or inactivation of microscopic organisms and pathogenic microorganisms is known as water disinfection.