The process of desalination of seawater on commercial vessels is a vital event in the daily life of the crew. As a result of the rapid developments in ballast water treatment operations, the question of whether ballast water treatment systems can be used as the main desalination system in the daily life of the crew on commercial vessels has been raised. This study introduces the current desalination systems on commercial vessels and their evaluation criteria. According to the literature and our professional industrial research, there are three most suitable alternatives such as “freshwater generator,” “reverse osmosis method,” and “attaching additional membrane filter to mechanical and ultraviolet (UV) ballast water treatment system.” Similarly, the evaluation criteria are determined as “installation cost of the system,” “operational cost of the system,” “risk of the system polluting the environment,” “risk of the system harming the human health,” “ease of repair and maintenance of the system,” “ease of use of the system,” and “ease of installing the system on the ship.” Due to the need for field expertise, we conducted several rounds of expert consultations. The novelty of this study is twofold. First, we improved the intuitionistic fuzzy TOPSIS (IF-TOPSIS) method by extending an expert prioritization technique. We also used an intuitionistic fuzzy scale for the expert weights. Second, as far as we know, this is the first study that employs an improved IF-TOPSIS method for desalination systems on commercial vessels. Moreover, we compared the proposed method and other methods to analyze the results. Results show that “freshwater generator” is more promising than “attaching additional membrane filter to mechanical and UV ballast water treatment system” that is prior to “reverse osmosis method.” This study helps the users and authorities understand the evaluation and select the desalination systems.