Changes in regulations and development of new technologies have affected the selection of alternative for treated wastewater disinfection. Disinfection is the last barrier of wastewater reclamation process to protect ecosystem safety and human health. Driving forces include water scarcity and drinking water supply, irrigation, rapid industrialization, using reclaimed water, source protection, overpopulation, and environmental protection. The safe operation of water reuse depends on effluent disinfection. Understanding the differences in inactivation mechanisms is critical to identify rate-limiting steps involved in the inactivation process as well as to develop more effective disinfection strategies. Disinfection byproducts discharged from wastewater treatment plants may impair aquatic ecosystems and downstream drinking-water quality. Numerous inorganic and organic micropollutants can undergo reactions with disinfectants. Therefore, to mitigate the adverse effects and also to enhance that efficiency, the use of alternative oxidation/disinfection systems should be evaluated as possible alternative to chlorine. This review gives a summary of the traditional, innovative, and combined disinfection alternatives and also disinfection byproducts for effluent of municipal wastewater treatment plants.