The classical mass balance equation is usually used to model the transfer of humidity in unsaturated macroscopically homogeneous porous media. This equation is highly non-linear due to the pressure-dependence of the hydrodynamic characteristics. The formal homogenization method by asymptotic expansions is applied to derive the upscaled form of this equation in case of large-scale heterogeneities of periodic structure. The nature of such heterogeneities may be different, resulting in locally variable hydrodynamic parameters. The effective capillary capacity and the effective hydraulic conductivity are defined as functions of geometry and local characteristics of the porous medium. A study of a two-dimensional stone-mortar system is performed. The effect of the second medium (the mortar), on the global behavior of the system is investigated. Numerical results for the Brooks and Corey hydrodynamic model are provided. The sensitivity analysis of the parameters of the model in relation to the effective hydrodynamic parameters of the porous structure is presented.