Numerical simulation of sediment transport is a coupled problem based on computation of profiles of water velocity and suspended sediment concentration. Effects of the water velocity profile and turbulent pulsation on vertical motion of suspended particles are emphasized in this study. Explanation of amplified sediment deposit in zones of separated flow near both natural and manmade bottom irregularities (like walls of shipping channels) is given. A semi-empirical approach to determination of long-term sediment deposit/erosion is suggested.