Inland waterways are an environmentally friendly and efficient mode of transport. At locations along the Nile River, Egypt, navigation is hindered requiring expensive, resource-intensive corrective. An increasing number of navigational bottlenecks have occurred between 1982 and 2015 because of changing river channel morphologies. This study provides a suitable method for evaluating navigation conditions within a reach of the Nile River. A 2D morphological model combined with a geographic information system application was created to assess the navigability of a reach of the Nile River, and different maintenance strategies were evaluated. Different scenarios of varying water levels, dredging operations, flow discharge fluctuations, and river channel morphological changes were considered. Results reveal that dredging operations, alone, cannot be adopted as a permanent solution for navigation bottlenecks, with the riverbed returning to its original state within 10 years. An important output of the method is the generation of reach scale hydro-morphodynamic maps that show the main morphological features, navigation bottlenecks, and navigation conditions. These maps aid in the development of strategic navigability plans and in evaluating long-term improvement measures. The method presented is applicability to large river systems worldwide.