Hyporheic zone is a region beneath and alongside a stream, river, or lake bed, where there is mixing of shallow groundwater and surfacewater. Hyporheic exchange controls a variety of physical, biogeochemical and thermal processes, and provides unique ecotones in a aquatic ecosystem. Field and experimental observations, and modeling studies indicate that hyporheic exchange is mainly in response to pressure gradients driven by the geomorphological features of stream beds. In the reach scale of a stream, pool-riffle structures dominate the exchange patterns. Flow over a pool-riffle sequence develops recirculation zones and stagnation points, and this flow structures make irregular pressure gradient which is driving force of the hyporheic exchange. In this study, 3 D hydro-dynamic model solves the Reynolds-averaged Navier-Stokes equations for the surface water and Darcy’s Law and the continuity equation for ground water. The two sets of equations are coupled via the pressure distribution along the interface. Simulation results show that recirculation zones and stagnation points in the pool-riffle structures dominantly control the upwelling and downwelling patterns. With decrease of recirculation zones, length of donwelling zone formed in front of riffles is reduced and position of maximum downwelling point moves downward. The numerical simulation could successfully predict the behavior of hyporheic exchange and contribute the field study, river management and restoration.