In recent years, the effects of natural environmental degradation have been significantly felt on the world's oceans. Studies show that both human-made pollutants like plastics and marine organisms such as invasive species are now densely present in our seas. On the other hand, the cooling water systems, a critical component of ships, rely on seawater absorbed through the ship's sea chests. However, clogging sea chests due to marine pollution can render the ship's main and auxiliary engines inoperable, depriving the ship of its maneuverability. A ship that loses its main engine power and therefore its maneuverability is at risk of facing accidents such as collisions, groundings, fires, and explosions. This study conducted a risk analysis on the blockage of sea chests, a hidden threat of marine pollution. Using both Classical and Fuzzy Failure Mode and Effects Analysis (FMEA) methodologies, risks were quantitatively calculated through Risk Priority Numbers (RPN) and Fuzzy RPN (FRPN) scores. According to the Traditional FMEA findings, the top three highest-risk failure modes are HT006- Main Engine High Lubricating Oil Temperature (143.520), HT007- Main Engine High Jacket Water Temperature (111.720), and HT014- Fire Pump Low Outlet Pressure and Flow Rate (100.590). The Fuzzy FMEA results indicated the top three highest-risk failure modes as HT006- Main Engine High Lubricating Oil Temperature (5.58), HT014- Fire Pump Low Outlet Pressure and Flow Rate (5.51), and HT013- Insufficient Boiler Steam Condensate Efficiency (5.47). The obtained findings quantitatively demonstrate the impact of marine pollution on ship systems. Analysis results provides critical information for key maritime stakeholders such as seafarers, maritime companies, regulatory authorities, and the shipbuilding industry to prevent major maritime accidents caused by sea chest blockages in the future.