For the computation of flow field and bed evolution in a water reservoir during the flushing process a fully three-dimensional hydrodynamic model, using a finite volume method to solve the Reynolds averaged Navier–Stokes equations, has been developed and combined with a three-dimensional sediment transport model. The hydrodynamic model is based the equations of mass and momentum conservation along with a standard k–e turbulence closure model. The sediment transport model is based on the equation of convection/diffusion of sediment concentration and sediment continuity equation for calculating the sediment concentration and bed level change in the reservoir flushing process, respectively. Both the hydrodynamic and sediment transport models are developed in a boundary-fitted curvilinear coordinate system. The grid is adaptive in the vertical direction, and changes according to the calculated bed level. The hydrodynamic section of the model was verified using experimental and direct numerical simulations data, and the sediment concentration calculations compare well with the experimental results. Also a physical model study was carried out to verify the results of bed evolution at the upstream of a sluice gate. Good agreement is found between bed evolution in the numerical and physical models.