A hydro-mechanical model of a heterogeneous granular bentonite mixture is presented based on discretization into a finite number of “bentonite units”, systems in which “megapores” are considered between bentonite grains, which, in turn, contain micro- and macropores. A macroscopic approach is used, where pore levels are associated with superposed homogeneous continua. Mixture heterogeneity is incorporated into the model considering the potentially very different percentage of megapores and grains in adjacent bentonite unit pairs. Mechanical contact is therefore affected, so a strategy is proposed based on porosity values, controlling deformability by the most deformable of the two units in contact.The constitutive formulation was implemented on a numerical solver to simulate a confined hydration test on a granular bentonite mixture with a notable initial local heterogeneity. The reproduced experimental evolution of the swelling pressure, relative humidity distribution, and water inflow was satisfactory. Porosity variation data were synthesized through histograms, describing not only the variation of the maximum and minimum porosity values but also the evolution of the porosity distribution in the mixture. This provides a quantitative description of the homogenization process, allowing an assessment of its scope and technological interest.