Layer-by-layer adsorption allows the creation of versatile functional coatings for ion exchange membranes, but the stability of the coating and resulting properties of modified membranes in their operation is a frequently asked question. This paper examines the changes in voltammetric curves of layer-by-layer coated cation exchange membranes and pH-metry of desalination chamber with a studied membrane and an auxiliary anion exchange membrane after short-term tests, including over-limiting current modes. The practical operation of the membranes did not affect the voltammetric curves, but enhanced the generation of H+ and OH- ions in a system with polyethylenimine modified membrane in Ca2+ containing solution. It is shown that a distinction between the voltammetric curves of the membranes modified and the different polyamines persists during the operation and that, in the case of polyethylenimine, there is an additional zone of growth of potential drop in voltammetric curves and stronger generation of H+ and OH- ions as indicated by pH-metry.