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This work presents a novel intelligent control system based on a Genetic Neuro-Fuzzy tool to optimize and improve the performance of a seawater reverse osmosis desalination plant (SWRO) on board a marine vessel. This investigation pays special attention to minimizing energy consumption to improve the energy efficiency of this marine installation. The system analyzes measurements of different variables—seawater pH, seawater conductivity, permeate flow rate, permeate conductivity, and total energy consumed—in order to provide the most appropriate value of permeate flow rate control and operating pressure of the high-pressure pump (HPP). This intelligent method allows the plant to achieve output values nearer to the desired setpoints set by the plant operators.