The present investigation pertains to modeling of seawater desalination system. A simulation model was developed and verified for a small-scale reverse osmosis system. The proposed model combines material balances on the feed tank, membrane Module and product tank with membrane mass transfer models. Finally a comprehensive simulation model has been developed incorporating the effect of mass transfer inhibition The model is non-linear differential equation representing the feed concentration as a function of operating time and space. The solution of the simultaneous differential equations was obtained using the fourth order Runge-Kutta method, due to self starting and stability. The model was verified using the experimental data from the literature [ 17,24]. Parameter sensitivity was carried out to select the proper step size. The simulation was run for over 1000 h enabling a prediction of operational performance at high overall system recoveries.