An integrated model on mixing flow, heat transfer, and BOD removal in a large scale wastewater treatment lagoon is presented. The flow model will be developed with multiphase flow theory, in which the multiple mixers are treated as momentum sources, and the effect of wind speed on the water surface is included. The heat exchange between the lagoon walls and surrounding ground, weather conditions, and solar radiations will be included into the heat boundary conditions for the heat transfer model. The flow and temperature fields will be simulated by Fluent CFD (computational fluid dynamics) commercial software. RTD (residence time distribution) in the lagoon will be predicted by solving scalar transport equation based upon the converged flow fields. BOD (biochemical oxygen demand) removal in the lagoon will be developed on the basis of first-order kinetics, and simulation of BOD removal will be conducted through coupling temperature and RTD.