The Damietta branch is considered one of the first-class waterways in Egypt. It is also a vital part of the VICMED project, which connects Lake Victoria to the Mediterranean Sea, achieving the shortest linking paths between the Nile Basin countries and Europe. Damietta branch exposed to many morphological changes since Aswan High Dam construction and human interventions such as river rehabilitation, water station intakes, and frequent dredging operations. All of that are affecting the branch behavior and stability. The current research is evaluating the morphological changes of Damietta branch over the years, and their effect on the waterway in reach bounded by Delta Barrage and Zefta Barrage to identify the locations of erosion and sedimentation, consequently navigational bottlenecks locations. Data were collected in the period 1982, 2009, 2014, and 2020. SMS and Civil 3D were used in the process of evaluating morphological changes. Then a two-dimensional (SRH-2D) model has been applied to determine the navigational bottlenecks that might occur in the lower flow conditions and their frequency in different years. It concluded that the sedimentation rate from 1982 to 2009 was around 0.2 m/year, while the years 2009 to 2014 was about 0.25 m/year and during the period 2014 to 2020 it was 0.5 m/year. These results showed that the stream has become more reactive and less stable with the continuous maintenance of navigation, and the sediments represented in the increase in the size of the islands. Therefore, the study accordingly recommended eluding wide-ranging dredging for its adverse implications.