In Northwest China, the sediment concentration of the Yellow River is high. A project to investigate the operation of a pumping station shows that the flow patterns in the forebay and inlet tank are disordered, and there is sediment deposition that endangers the normal operation and safety of the pumping station. To solve this problem, the three-dimensional two-phase water-sediment flow in the forebay of the pumping station is modeled by using fluid simulation software, and diagrams of the sediment volume fraction content and vector distribution in the flow layers of different sections are obtained. Combined with the multiphase flow theory of mixtures and the realizable turbulent kinetic energy equation, the location and formation mechanism of each vortex, as well as the area and degree of sediment deposition in the forebay, are analyzed. The actual engineering and numerical simulation results are compared to verify the accuracy of the simulation. The results show that the main reason for sediment deposition is the high sediment concentration of the Yellow River, but the flow pattern disorder is affected by a specific design defect of the forebay, which makes the sediment deposition worse. The results of this study provide specific guidance and methods for the construction and transformation of the forebay of the pump station in the future; construction to weaken the return area to a certain extent can reduce the degree of sedimentation.