Abstract: The key to study turbulence problems in reality by using numerical simulation is to take into account discrepancy of the Reynolds Stress.A 3-D anisotropic algebraic stress model (ASM) is established successfully to simulate turbulence driven secondary flow in natural channel.Comparison between the calculated results and experienced results in rectangular ducts has certified the high accuracy of the numerical model.Combining the ASM with unstructured meshes results in more reasonable out come than ever before for open channels with complicate sandpit The ASM is a powerful tool to study stability and deformation of riverbeds.The analyzes show that not only the streamwise flow scours the upstream edge of the sandpit but also the sec ondary current erodes transversal part of the cross section.However,studies in its turbulence characteristic indicate that a sandpit has severe effect on riverbed stability.