Due to their prevalence in the lithosphere and their high capability of sorbing pollutants, smectite clays play a foreground role in environmental pollution studies, waste management and soil science. In complementarity with existing approaches at the molecular or macroscopic scales, real microstructures have been employed to investigate ionic transport by diffusion through montmorillonite and water-saturated Wyoming bentonite at intermediate scales ranging between the nanometer and the micrometer. The coupled solute transport and electrostatic phenomena investigated at the nanopore scale are upscaled using the Homogenization of Porous Media approach. Homogenization computations rely on a hierarchical description of bentonite that acknowledges the existence of pores networks at different scales. At the scale of montmorillonite layers, digitized TEM images have been employed to simulate diffusion of ionic solutes by considering electrostatic interactions in the vicinity of the negatively-charged clay platelets' surface. Finite Element microstructures are created after extraction of the contours of the layers using dedicated image processing algorithms. Local electric potential distribution, anion exclusion and cation inclusion are displayed by ion distribution maps. The effective diffusion tensor and the transport equation obtained through volume averaging are then used to simulate diffusion at the scale of a Wyoming bentonite sample composed of clay gels of variable density, solid grains and micropores. Qualitative comparisons were made with existing diffusion data, and a particular attention is given to the anisotropy of the diffusion tensors at both the mesoscopic Diffusion calculations on reconstructed bentonite microstructures and macroscopic scales.