Since the transportation of goods and merchandise is widely performed by ships, a huge amount of energy is required for sea vessels. This paper provides a detailed analysis of energy efficiency and the effects of environmental pollution on ships. It also investigates the effect of pollution on the main engines of ships and their cooling systems. The concepts put forward here are based on data recorded six times a day for 79 days before and after the cleaning process. It was observed that when the factor of pollution was eliminated, the temperature of the cylinder jackets went down considerably to an average rate of 3.5%. Heat transfer also increased in water circuits in main engine cylinder jackets by an average rate of 25.94%. The heat transfer increased by an average rate of 52.622% in sea water circuit. It increased by an average rate of 20.32% in the scavenge circuit. In addition, it increased by an average rate of 23.55% in freshwater circuits. The amount of distilled water production increased at a rate of 30%. In addition, the seawater circuit of the main engine cooler was polluted at a different rate and simulated with a simulator.