This study comprehensively explores the intricate hydrodynamic and geomorphological processes that affect the Sulina Channel and bar area. It employs advanced hydrodynamic, wave, and sediment transport models to simulate the influence of marine currents, waves, and shipping traffic on sediment transport and deposition patterns, providing valuable insights for maintaining navigable conditions in the Sulina Channel. It is shown that sediment deposition is highly dynamic, particularly in the Sulina bar area, where rapid sediment recolonization occurs within one to two months after dredging. The simulation indicates that vessels with drafts of 11.5 m cause notable erosion. In comparison, drafts of 7 m have a minimal impact on sediment transport, emphasizing the importance of managing vessel drafts to mitigate sediment disturbances. This research highlights and quantifies the siltation phenomenon from the Black Sea to the mouth of the Sulina Channel, effectively addressing the challenges posed by natural and anthropogenic factors to ensure the Channel’s sustainability and operational efficiency.