The use of nanofiltration as a pretreatment step in a zero rejection process was investigated. Nanoflux, a nanofiltration simulation software, was used to predict the rejection of Co2+ and Ni2+ from a salty multi-element matrix whose concentration is similar to seawater. Orientation simulations prior to filtration experiments were made with Nanoflux in order to predict ionic rejections. Previously, the multi-element matrix solution speciation was studied by JChess. It was shown that the effective membrane charge and the effective membrane thickness, adjusted through the filtration of a single salt NaNO3 solution, could be used to predict the ionic rejections of the multi-element solution for two commercial nanofiltration membranes. The elevated concentration of NaNO3 in the multi-electrolyte solution did not reduce the high ionic selectivity of divalent ions. Predicted values were in good agreement with experimental results at neutral pH of the multi-electrolyte solution.