In the present study, considering the transport and transformation processes of variables, a threedimensional water quality model for the river system was established, which coupled the volume of fluid (VOF) method with the k-ε turbulence mathematical model. Then, the water hydrodynamic characteristics and transport processes for BOD5, NH3-N and TP were analyzed. The results showed that the water surface of convex bank was a little lower than that of concave bank due to the centrifugal force near the bend, and most concentrations were inferior to the type Ⅴ standard indexes of surface water environmental quality. The model validation indicated that the errors between the simulated and monitored values were comparatively small, satisfying the application demands and providing scientific basis and decision support for the restoration and protection of water quality.