The Nile River is recognized as an alluvial river with high morphological changes. Sedimentation is a key issue affecting the management of water resources. Concerning navigation, the problem of lack of appropriate depths for the movement of ships is observed, especially in periods of lower water levels. This study aims to investigate the morphological changes, improve the flow characteristics, and solve sedimentation issues in front of a proposed navigation dock in the Nile River. Sediment buildup causes a decrease in water depth and flow rates, making navigation more difficult and raising maintenance expenses. This study discussed the evaluation and implementation of solutions to enhance flow velocities, minimize sediment deposition, and improve the navigability and sustainability of the riverine transportation system. A built and calibrated two-dimensional mathematical model SMS was used to simulate morphological changes at the studied river reach affected by deposition. The solutions can be summarized as dredging around the study area in front of the navigation dock to solve the problem of the lack of appropriate depths for anchoring the units, using spur dikes on the western bank to direct the flow to the study area, and combinations of both dredging and using spur dikes. Twenty-two alternatives were studied in the case of average discharge. Two best solutions including both dredging and using spur dikes were concluded. The two best alternatives were studied in the cases of max. and min. discharges and proved to be effective solutions.