Sedimentation plays a key role in determining the morphology of a river. The river changes its bed because of hydrodynamics resulting from variabilities of the flow. Sedimentation in Mississippi River and its tributaries have been a topic of major concern. Sedimentation phenomenon is followed by erosion and deposition in the river and changes the river geometry continuously with the changing discharge and sediment properties. The erosion and deposition makes the design and operation of a physical infrastructure such as dams, locks, and levees a challenging task. The study of sediment movement in the Mississippi River can help in better operation of infrastructure and planning for appropriate mitigating measures. The current model utilizes the National Center for Computation Hydroscience and Engineering 2D tool, also known as CCHE2D, for modelling the transportation of sediments at the upstream location of United States Geological Survey streamflow station 07022000 Mississippi River at Thebes, Illinois. Although the 2D model requires more computation time but is effective in incorporating spatial river features as they impact the hydrodynamics and sedimentation. The model results evaluated the river morphology variations for maximum long term mean monthly flow due to sediment transport. The results also include the hydraulic flow variables estimations by numerical modelling. The results obtained from the study can help hydraulic engineers for sediment and flow management.