Transport and separation processes in ionic systems located in the porous medium are investigated. The software for the modeling of the combined electroosmotic, migration, diffusion and pressure driven flow in the spatially 2D or 3D porous medium has been developed. This software allows to determine the mapping from the parametric space of the porous structure and distribution of fixed charge into the space of application properties such as ionic permselectivity or perfusion flow. Software capabilities are illustrated on case studies of systems where the Debye length is either comparable or negligible with respect to the characteristic pore size. The concept of the reconstructed porous medium has been employed to represent the morphology.