In this work we combine existing ideas on gravel and sand entrainment into a simulation model for flows that flush sand from the surface and subsurface of a gravel riverbed. A flume experiment is conducted to provide a test of the flushing model. The primary advance represented in this paper is incorporation of a two-fraction entrainment approach into a routing model to account for the effect of sand content on the entrainment and transport of bed sediment, which is crucial for simulation of the flushing process associated with progressively decreasing sand proportions. A combination of the active layer concept and two-layer treatment is adopted herein to outline the framework of sediment transport system, which allows incorporation of subsurface sand into the surface layer through the mechanisms of upward entrainment and bed degradation. Sediment routing computations are executed in two steps: in the first step, the change of bed level is computed with the continuity equation of sediment in the surface layer; in the second step, the changes of sediment storage in the surface and subsurface layers are calculated with the mass conservations of sediment. An important finding of this study is that the flume results could not be adequately simulated without an upward sand flux from the subsurface, which confirms the operation of a process that has only been hypothesized. The simulation results, including the evolutions of bed composition and elevation, are in good agreement with the observations, implying a potential application of the proposed model in determining flushing flows for environmental benefit.