Sediment and deposition are among the main problems in dam engineering and other related fields. Because of the numerous advantages of numerical modeling, effects of different geometries of reservoirs on the flow pattern and deposition of sediments are investigated using the finite volume based Flow-3D software package. In this study, three rectangular reservoirs with different dimensional ratios are simulated using the large eddy simulation (LES) turbulence model. To validate the numerical modeling, existing experimental data is used. Results indicate that Flow-3D can accurately simulate flow and sediment deposition in the reservoirs, and the numerical data are in reasonable agreement with the experimental results. Numerical efforts showed that the amount of deposition in reservoirs is significantly dependent on the geometry. Among the modeled reservoirs, the 6 × 4 m one has the best performance. Moreover, it can be said that changing the position of the flow’s inlet and outlet of the reservoir does not have a considerable effect on increasing its efficiency.