The Preissmann implicit scheme is used to discrete the one-dimensional Saint-Venant equation and the river-junction-river method is applied to resolve the hydrodynamic mathematical model for river networks. Based on the characteristics of river-junction-river method and the theory of WASP, the synthetic water quality model is set up for river networks, which includes many contamination variables and considers the transform and transplant of the contamination variables. This model is applied to simulate four river networks, the results of elevations and flows agree with the data, the result of contamination variables agree with the measured data. These results show this model is credible and it is a practical tool for forecast and management of water quality in river networks.