The basic aim of this work is to present a combination of techniques for the reconstruction of the porous structure and the study of transport properties in porous media. The disordered structure of porous systems like random sphere packing, Vycor glass and North Sea chalk, is represented by three-dimensional binary images. The random sphere pack is generated by a standard ballistic deposition procedure, while the chalk and the Vycor matrices by a stochastic reconstruction technique. The transport properties (Knudsen diffusivity, molecular diffusivity and permeability) of the resulting 3-dimensional binary domains are investigated through computer simulations. Furthermore, physically sound spatial distributions of two phases filling the pore space are determined by the use of a simulated annealing algorithm. The wetting and then on-wetting phases are initially randomly distributed in the pore space and trial-and-error swaps are performed in order to attain the global minimum of the total interfacial energy. The effective diffusivities of the resulting domains are then computed and a parametric study with respect to the pore volume fraction occupied by each phase is performed. Reasonable agreement with available data is obtained in the single- and multi-phase transport cases.