Pumping stations serve as critical hydraulic infrastructure for water conveyance and irrigation. Sediment deposition in forebays can deteriorate intake flow conditions, increase hydraulic losses, reduce pumping efficiency, and consequently impair the long-term operational performance of pumping systems. To accurately predict sediment deposition in complex three-dimensional flow fields, we developed a dynamics-driven boundary-responsive numerical model that integrates sediment particle dynamics with real-time bed evolution. This model adopts the near-bed vertical velocity of sediment particles as the deposition discrimination criterion and dynamically updates bed topography via a mass-conservation-based boundary response strategy. The proposed method was validated against open-channel experimental data. The simulated flow structures, deposition patterns, and temporal variations in deposition thickness agreed well with the measurements, with average deviations below 4%. Compared with conventional static-boundary numerical methods, the proposed model reproduces the coupled evolution of sediment transport, flow redistribution, and bed deformation with higher fidelity. The developed framework provides an effective numerical tool for sediment deposition prediction and offers practical support for hydraulic structure optimization, maintenance scheduling, and energy-efficient operation of pumping stations with sediment-laden flow.