Ammonia and COD are selected as study variables for they are the main water quality parameters and can represent water environment quality of the Harbin City Reach of the Songhua River. One-dimensional water quality model is used to set up the relationship of pollutant loadings and water quality. The comprehensive decay rate (k), a key parameter of water quality model, is estimated by Bayesian method. The seasonal model and annual model are respectively set up according to different k estimated in different period. The pollutant loadings are controlled by the models for downriver water quality can meet targeted goals. From contrasting the two models, it indicates that predicting precision of seasonal model is high than annual model for seasonal model can better express comprehensive degradation concentration of ammonia in water. Contrasting with other methods, water quality management with seasonal model can offer decision makers more useful information, and help them address uncertainties. In addition, influencing weights of the three pollution sources can be obtained by contrasting load reduced ratios. The information could inform decision makers of the required load reductions for the three time periods.