The underperforming treatment plants are pathways for transmission of infectious disease like Hepatitis E Viruses (HEV) which poses global health threat. The sewage treatment plant situated in hilly and cold climate of Shimla was underperforming which caused various episode of HEV induced jaundice outbreak thus in this research performance evaluation an efficient tool is used to identify the operational challenges of sewage treatment. The stratified sampling is used to determine the physiochemical parameters of inflow-outflow of each process to assess the performance of sewage treatment. The overall removal efficiency of Chemical Oxygen Demand (COD), Biochemical Oxygen Demand (BOD5) and Total Suspended Solids (TSS) are found to be 82%, 75% and 79% respectively which was lowered by 10 to 15% during winter season. Topographical undulation and flow variation might be the reason of shock load and significantly high flow velocity. High strength sewage and lowered bioactivity during cold weather has caused poor quality effluent which might be enhanced by optimal dosage of alum in clariflocculator. Virus load test and optimum disinfection of effluent may restrict viruses to cause disease outbreak. Present research indicates that similar field study can achieve the social sanitation and conservation of river in developing countries.