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In this study, we conducted a numerical simulation to evaluate stability in the seawater reverse osmosis (SWRO) process against seasonal variations of feed water. The impact of element configuration on SWRO operation was analyzed using a process model consisting of the solution–diffusion model. Seawater quality and temperature data collected from the intake of the Fujairah desalination plant (United Arab Emirates) were used to identify optimum internally staged design (ISD) configurations. Monitoring data were also used to simulate changes in SWRO performance. The process performance of the ISD configurations as compared to conventional design configurations in terms of specific energy consumption, permeate total dissolved solids concentration and recovery ratio. The results showed that SWRO processes with four ISD configurations met the performance requirements over 12 months despite the fluctuations in seawater quality and temperature. The pre-diction results of the ISD configurations showed stable operation during the 12 month simulation period. These configurations had a significant advantage with respect to membrane maintenance. This study’s findings could be used to optimize the element configuration of the SWRO process by predicting the process performance while accounting for seasonal variations of seawater quality and temperature.