This paper presents a three-dimensional (3D) mathematical model for suspended load transport in turbulent flows. Based on the stochastic theory of turbulent flow proposed by Dou, numerical schemes of Reynolds stresses for anisotropic turbulent flows are obtained. Instead of a logarithmic law, a specific wall function is used to describe the velocity profile close to wall boundaries. The equations for two-dimensional suspended load motion and sorting of bed material have been improved for a 3D case. Numerical results are in good agreement with the measured data of the Gezhouba Project. The present method has been employed to simulate sediment erosion and deposition in the vicinity of the Three Gorges Dam. The size distribution of the deposits and bed material, and flow and sediment concentration at different times and elevations, are predicted. The results agree well with the observations in physical experiments. Thus, a new method is established for 3D simulation of sediment motion in the vicinity of dams.