This study simulates an RO system for seawater desalination to overcome Iran’s water crisis due to drought and increasing demand. Based on previous studies, a scientific gap has been observed in that the effect of single‐stage or two‐stage systems on performance and effective parameters has not been investigated. In addition, examining the types of arrangements for using pressure vessels will make the present study more comprehensive. SW30XHR‐440i modules are used for desalination and three different feed flow rates (800, 1200, and 1600 m3/day) and three different recovery percentages (40, 55, and 70%) are used for sensitivity analysis. The methodology of the solution includes the examination of different configurations and the solution of the transport equations in the Water Application Value Engine (WAVE) 1.82 software. The configurations without technical errors are selected as the answer for further investigation and comparison with each other. The results show that the lowest specific energy of the pump with the amount of 4.18 kWh/m3 corresponds to the 55% recovery of the two‐stage system (800 m3/day permeate flow rate). As a general result, it can be stated that as the flow rate increases, the advantage of using a 6‐element pressure vessel over an 8‐element pressure vessel becomes more significant. Also, using the two‐stage system instead of single‐stage system is less feasible for higher permeate flows.