A numerical study of the three-dimensional turbulent flow, which develops over bed dunes in an open channel of finite width, is presented. Fluid motion is governed by the three-dimensional Reynolds-Averaged Navier-Stokes (RANS) equations and turbulence is modeled by means of the k-ε closure model. The presence of the channel sidewalls has a strong effect on flow characteristics such as the free-surface elevation, velocity, wall stress, turbulence and streamwise vorticity.