A one-dimensional numerical model (HEC-RAS) was calibrated to simulate morphological changes in the study reach of the Nile River downstream of Esna barrages by using the available field data of the years 2010 and 2013. The presented research utilizes the synergies between GIS and HEC-RAS in studying the morphological changes in the study area that affects directly the navigation condition and Proposes the optimum navigation path in the selected study reach based on the numerical model results data. Using data measurements, the model was calibrated and verified. It gave a reasonable agreement between the calculated and measured values for the water level and the morphological changes in the selected cross-sections and along the River's thalweg with accuracy 99.63% and 96.66% for hydraulic and sediment calibration and verification. It can be concluded from several runs of the model that the best equation for predicting morphological changes within the study area is the Ackers-White equation. Finally, the results indicate that the HEC-RAS model presents a satisfying performance for sediment transport.