This study developed a one-dimensional model for a bipolar membrane unit used in desalination stacks with the finite– element method (FEM) based Comsol Multiphysics software. The numerical model took into account the stationary transport of K+, Cl-, H+ and OH- ions inside a desalination channel unit using Nernst – Planck – Poisson equations and the Onsager theory of the Second Wien Effect for water dissociation under externally applied electrical fields. Electrochemical behaviour for the unit cell model was validated through the experimental current-voltage curve of a bipolar membrane, as it was reported in the literature. Influence of the anion–exchange layer (AEL) and cation–exchange layer (CEL) thickness variation and fixed charge concentration ratio in CEL/AEL regions upon specific desalination performance parameters, like co–ion leakage current, water dissociation turn-on voltage and water dissociation resistance were investigated here. Evolution of K+, Cl-, H+ and OH- ion concentration through specific compartments on the unit cell (electrolyte, AEL, CEL) at different potential drops across the membrane helped to understand the contribution of specific ionic fluxes at the total current through the system.