Modelling of salt transfer processes in fractal structured media has been considered on the base of fractional derivative equations with Caputo-Gerasimov derivatives with respect to space variables. Initial-boundary problem has been solved using locally one-dimensional finite difference scheme. Procedure of fractional derivative approximation has been proposed to lower computational complexity of solution process. Parallel algorithms for distributed memory systems and GPU have been considered. Analysis of using one-dimensional and red-black data partitioning schemes is presented and new parametric scheme which have better characteristics in the determined conditions has been proposed.