Disinfection is considered to be the primary mechanism for the inactivation/destruction of pathogenic organisms to prevent the spread of waterborne diseases to downstream users and the environment. It is important that wastewater be adequately treated prior to disinfection in order for any disinfectant to be effective.

The most commonly used disinfectant for both drinking water and wastewater treatment is chlorine. Its effectiveness against a wide spectrum of disease causing organisms, relatively low cost, and high reliability contribute to its popularity. Chlorine can be applied to water directly as a gas, or through the use of chlorinating chemicals. A number of alternative disinfectants, such as chlorine dioxide, chloramines, ozone, and ultraviolet radiation, are also used to varying degrees.

Each disinfection technology has unique benefits, limitations, and costs. Individual water system operators must weigh these trade-offs and choose disinfection methods based on local water quality conditions and the needs and resources of the communities they serve.