Disinfection of treated sewage aims to kill pathogens (disease-causing microorganisms) prior to disposal. It is increasingly effective after more elements of the foregoing treatment sequence have been completed. The purpose of disinfection in the treatment of sewage is to substantially reduce the number of pathogens in the water to be discharged back into the environment or to be reused. The target level of reduction of biological contaminants like pathogens is often regulated by the presiding governmental authority. The effectiveness of disinfection depends on the quality of the water being treated (e.g. turbidity, pH, etc.), the type of disinfection being used, the disinfectant dosage (concentration and time), and other environmental variables. Water with high turbidity will be treated less successfully, since solid matter can shield organisms, especially from ultraviolet light or if contact times are low. Generally, short contact times, low doses and high flows all militate against effective disinfection. Common methods of disinfection include ozone, chlorine, ultraviolet light, or sodium hypochlorite. Monochloramine, which is used for drinking water, is not used in the treatment of sewage because of its persistence. 
Chlorination remains the most common form of treated sewage disinfection in many countries due to its low cost and long-term history of effectiveness. One disadvantage is that chlorination of residual organic material can generate chlorinated-organic compounds that may be carcinogenic or harmful to the environment. Residual chlorine or chloramines may also be capable of chlorinating organic material in the natural aquatic environment. Further, because residual chlorine is toxic to aquatic species, the treated effluent must also be chemically dechlorinated, adding to the complexity and cost of treatment.
Ultraviolet (UV) light can be used instead of chlorine, iodine, or other chemicals. Because no chemicals are used, the treated water has no adverse effect on organisms that later consume it, as may be the case with other methods. UV radiation causes damage to the genetic structure of bacteria, viruses, and other pathogens, making them incapable of reproduction. The key disadvantages of UV disinfection are the need for frequent lamp maintenance and replacement and the need for a highly treated effluent to ensure that the target microorganisms are not shielded from the UV radiation (i.e., any solids present in the treated effluent may protect microorganisms from the UV light). In many countries, UV light is becoming the most common means of disinfection because of the concerns about the impacts of chlorine in chlorinating residual organics in the treated sewage and in chlorinating organics in the receiving water. 
As with UV treatment, heat sterilization also does not add chemicals to the water being treated. However, unlike UV, heat can penetrate liquids that are not transparent. Heat disinfection can also penetrate solid materials within wastewater, sterilizing their contents. Thermal effluent decontamination systems provide low resource, low maintenance effluent decontamination once installed.
Ozone () is generated by passing oxygen () through a high voltage potential resulting in a third oxygen atom becoming attached and forming . Ozone is very unstable and reactive and oxidizes most organic material it comes in contact with, thereby destroying many pathogenic microorganisms. Ozone is considered to be safer than chlorine because, unlike chlorine which has to be stored on site (highly poisonous in the event of an accidental release), ozone is generated on-site as needed from the oxygen in the ambient air. Ozonation also produces fewer disinfection by-products than chlorination. A disadvantage of ozone disinfection is the high cost of the ozone generation equipment and the requirements for special operators. Ozone sewage treatment requires the use of an ozone generator, which decontaminates the water as ozone bubbles percolate through the tank.
Membranes can also be effective disinfectants, because they act as barriers, avoiding the passage of the microorganisms. As a result, the final effluent may be devoid of pathogenic organisms, depending on the type of membrane used. This principle is applied in membrane bioreactors.