This study employs theory and experimental data from a laboratory-scale electrodialyzer to predict sodium chloride (NaCl) mass transport and concentration distribution along the electrodialyzer as a function of feed concentration, feed flow rate, applied voltage, and pressure. Moreover, a model was developed to predict the ion removal as a function of driving forces through solving the complete Navier–Stokes, continuity, and steady state Nernst–Planck equations by the finite difference numerical method. The findings of the experiments confirmed that concentration distributions are nonlinear along both the dilute and concentrate compartments. The results also demonstrated that increases in pressure and feed flow rate have a negative effect on salt removal, linear and nonlinear for pressure and flow rate, respectively. In the investigated ranges, higher voltage increased salt removal at a constant feed concentration.