In this paper a mathematical method to calculate longitudinal and vertical flow velocity and non-equilibrium concentration of suspended load in open channels with a trench is discussed. This method is based on 0-equation turbulence model and two dimensional diffusion equation of suspended sediment. Using this method, the velocity profiles and the concentration distributions are simulated for some trenches with different ratio of the depth to the length. These results show that the flow structure that consists of main flow and circular flow can be simulated precisely and the concentration can not be calculated correctly without the estimation of two dimensional flow structure.