In a majority of ports, a ship’s speed is limited for reasons of navigational safety. At the same time, captains and port pilots choose the speed of the ship, but it cannot be higher than the speed allowed in the port. Therefore, the speed of the ship also depends on the experience of the masters and harbor pilots and the sailing conditions in specific situations. Choosing the optimal speed of the ship in the port, considering the hydrodynamic effect of shallow water and the controllability of the ship, can help reduce fuel consumption and ship emissions, which is important for the development of a sustainable port. In all cases, the safety of the shipping is the highest priority. The main objectives of this article are determining the optimal speed of ships in ports with low clearance under a ship’s hull, ensuring navigational safety, reducing fuel consumption and emissions, and creating a sustainable port. This article presents the methodology for calculating the optimal ship speed as the minimum controllable speed, fuel consumption and emission reduction, as well as its implications for sustainable and green maritime transport and port development. The methodology presented has been tested on real ships and using a calibrated simulator, navigating through port channels and port water’s restricted conditions.