Effective diffusion tensors were computed for tracer diffusion through compacted water-saturated bentonite at two distinct scales by combining random microstructures and microstructures obtained by Transmission Electron Microscopy. The original micrographs have been thresholded by considering four distinct phases at the mesoscopic scale, and image analysis techniques have been employed in order to characterize the morphology and in particular the texture anisotropy of grains, clay gels and macrovoids. The Homogenization of Periodic Media approach employed is based on the local description ion diffusion at both the microscopic level of clay platelets (assuming variable diffusivity and ion sorption) and the mesoscopic level of clay aggregates and macropores. The local problems were successively solved using randon and TEM-based numerical microstructures in order to investigate the contribution to macroscopic diffusion of soft gels, dense gels and macrovoids under various configurations. Comparisons were made with existing diffusion data for montmorillonite and natural bentonite, and a particular attention was given to the anisotropy of the macroscopic diffusion tensor in connection with morphological characteristics of the underlying microstructure. The effect of clay matrix diffusivity on the magnitude and orientation of the macroscopic diffusion tensor has been investigated, and the principal axes of diffusion have been compared with the index of fabric orientation. Computations were also performed on microstructures of increasing size in order to investigate the model implicit assumption of existence of a Representative Elementary Volume.