This study suggests a novel 3D numerical model for simulating the flow and bed deformation around hydraulic structures, considering the transition process from bed-load motion to suspension. The numerical analysis of the fluid is carried out by solving the Reynolds-averaged Navier-Stokes (RANS) equations coupled with the Volume of Fluid (VOF) method. The temporal change in bed topography is calculated by coupling a stochastic model of sediment pickup, deposition, and transition and a momentum equation of sediment particles to account for the effect of non-equilibrium and transition from bed load to suspension. The numerical model was applied to an experimental scour phenomenon upstream of a slit weir, in which the initial bed elevation was lower than the crest elevation of the slit (i.e., all eroded particles experienced the transition process from bed load to suspension around the slit). A comparison between the numerical results and experimental data indicated that the model could reproduce the scour geometry around the slit weir with sufficient accuracy.