The effects of the seawater-intake temperature on the performance of the refrigeration system which exists on a cargo vessel were introduced in this study. The performance of the real refrigeration system was analysed by using both conventional and advanced exergy analyses and exergoeconomic evaluation. First, a parametric study with different seawater-intake temperatures was carried out by applying conventional exergy and advanced exergy analyses to the refrigeration system considered to identify the pinch point components and processes with high irreversibilities. Then, advanced exergy analyses were applied to overcome technological and physical limitations to increase the knowledge about the refrigeration system. The exergetic efficiency of the refrigeration system was calculated based on varying seawater-intake temperature which enters the condenser while other operating parameters are kept constant. Seawater-intake temperatures were selected in terms of regional seawater temperatures which are assumed to be in the vessel route. As a result of the study, it was determined that the hot entry of the seawater into the condenser causes a reduction in the exergetic efficiency of the refrigeration system. The gap between real system exergetic efficiency and the unavoidable cycle exergetic efficiency increased as the pinch point temperature differences increased in the condenser by approximately 16%. Some of the exergy destruction in the refrigeration system components was unavoidable and constrained by technological and physical limitations. Based on the findings in this study, it has been shown that the greatest improvement in the exergetic efficiency of the cooling system can be achieved by improving the condenser and compressor.