Knowledge of the correlation between the molecular polyelectrolyte structure of membranes and their transport properties helps to develop new ion-exchange polymers with improved characteristics. This research paper studies the transport properties of two counter-ions, H⁺ and Na⁺, inside four commercial cationic membranes with experimental methods: three aromatic hydrocarbon polymer membranes CM-1, CMX, MK-40, and one tetrafluoroethylene polymer Nafion analog membrane MF-4SK. Ab initio calculations of the membrane structures with various hydration levels were applied in order to interpret the difference in the transport parameters of counter-ions between aromatic hydrocarbon MK-40 and non-aromatic perfluorinated MF-4SK polymer membranes. The membrane physico-chemical characteristics and the conductivity were experimentally investigated as a function of NaCl and HCl aqueous solution concentration. The conductivity and diffusion coefficients of the counter-ions, as well as volume fractions of ‘gel’ and ‘inter-gel’ phases were determined based on the microheterogeneous two-phase model. For the first time, ab initio calculations on membrane models were correlated with experimental findings in order to explain the difference in the mobility of the two counter-ions. The static ab initio study indicates the dissociation of the functional groups and a stronger water connectivity in perfluorinated membrane, providing an explanation for the measured highest diffusion coefficient and molar conductivity of the counter-ions H⁺ and Na⁺ in MF-4SK membrane in comparison to MK-40 membrane.