Seawater nanofiltration (SWNF) generates a softened permeate stream and a retentate stream in which the multivalent ions accumulate, offering opportunities for practical utilization of both streams. This study presents an approach to simulation of SWNF including all major seawater ions (Na+, Cl-, Ca2+, Mg2+, and SO42-) based on the Nernst-Planck equation, and uses it for permeate and retentate streams composition prediction. The number of degrees of freedom in the system was reduced by assuming a very high ionic permeability for Na+, which only weakly affected the other parameters in the system. Two alternatives were examined to analyze the importance of concentration dependence of ion permeabilities: The assumption of constant ion permeabilities resulted in a reasonable fit with experimental data. However, for the permeate composition the overall fit was significantly improved (P < 0.0001) when the permeabilities of Ca2+ and Mg2+ were allowed to depend on the ratio of their total concentration to Na+. This type of dependence emphasizes the strong interaction of divalent ions with the membrane and its effect on the membrane fixed charge through screening or charge reversal. When this effect was included, model predictions closely matched the experimental results obtained, corroborating the phenomenological approach proposed in this study.