The present invention provides a sewer system having a means to quickly disinfect rainwater-incorporated sewage and pollutant-incorporated rainwater, that is, combined sewer overflow (CSO), separated sewer rainwater overflow and separated sanitary sewer overflow before being discharged to public water body without passing through a sewage treatment plant, and a method and an apparatus for disinfecting rainwater-incorporated sewage and pollutant-incorporated rainwater. One embodiment of the present invention is a sewer system wherein when sewage flows into a sewage treatment plant in an amount of not more than the treatment capacity of the sewage treatment plant, the sewage is subjected to predetermined treatments in the sewage treatment plant, and then disinfection with a chlorine-based disinfectant, and thereafter discharged to public water body, and when sewage containing rainwater in an amount of more than the treatment capacity of the sewage treatment plant flows or may flow into the sewage treatment plant by a big rainfall, the amount of the rainwater-incorporated sewage of more than the treatment capacity is branched in sewer stormwater overflow removing facilities of a sewer, then disinfected with a bromine-based disinfectant, and thereafter discharged to public water body while the rainwater-incorporated sewage in an amount within the treatment capacity of the sewage treatment plant is subjected to predetermined treatments in the sewage treatment plant, then disinfected with a chlorine-based disinfectant, and thereafter discharged to public water body.