Electrokinetic desalination techniques have been successfully applied for the prevention of salt-induced deterioration problems of masonry and other construction materials. A mathematical model for electrochemical desalination treatments is described, based on the Poisson-Nernst-Planck system of equations and accounting for the chemical interactions between the species in the pore solution and the solid matrix. Due to their high abundance in the natural environment, chlorides, nitrates and sulfates are considered the main ions responsible to the salt decay processes in buildings materials and sculptures. Simulations of the desalination treatment of brick samples contaminated with these target contaminants are shown. The influence of the chemical interactions on the efficiency is highlighted in the results.