In the present work, a mathematical model for exergy analysis of a two-pass sea water reverse osmosis (SWRO) desalination system has been developed using Engineering Equation Solver (EES) software and the developed model has been validated using data set reported in the literature. The minimum separation work has been found out as 154.35 kW and second law efficiency were found out as 18.3%. Total exergy destruction was 686.94 kW out of which major exergy destruction of 291.30 kW occurs in SWRO brine disposal, 210.32 kW in pumps, followed by 109.80 kW and 59.76 kW in SWRO and BWRO membranes, respectively. The results for exergy analysis match very accurately with the published results. It is suggested that the measures like use of energy recovery device for SWRO brine disposal, high-performance pumps having variable frequency drive features and high-performance membranes have potential for minimizing the exergy destruction.