In many ports, the ship's speed is limited for the safety of navigation. At the same time, ship captains and port pilots choose the speed of the ship, but not higher than the permitted speed of the ship in the port, therefore the speed of the ship also depends on the experience of the ship captains and port pilots and the sailing conditions of the ship in specific conditions. Choosing the optimal speed of ships in port, including the effect of shallow depth, can reduce fuel consumption and ship emissions in ports, which is important for the development of green and sustainable ports. In all cases, shipping safety is the highest priority. The main objectives of the article are determining the optimal speed of ships in ports with low clearance, ensuring navigational safety, reducing fuel consumption and emissions, and at the same time creating a sustainable port. The article presents the methodology of optimal ship speed calculation, minimum ship controllable speed maintenance, fuel consumption and emission reduction methodology and their impact on sustainable and green maritime transport and port development. The developed methodology was tested on real ships and with the help of a calibrated simulator, sailing through harbor channels and harbor waters in low clearance conditions.