Hydraulic conductivities of compacted water-saturated bentonite were computed based on the real microstructure. The Homogenization of Periodic Media approach employed fully acknowledges the heterogeneous and multiscale microstructure of clay, as well as locally varying physical flow properties. Consequently, three levels of description were considered : the microscopic level of clay particles, the mesoscopic level of clay aggregates, mineral grains and inter-aggregate porosity, and the macroscopic level of the sample subjected to fluid pressure gradients in the laboratory. Starting from the local description of fluid flow, the expression of the effective hydraulic conductivity tensor was derived. The soft and dense gels and the open voids may form a connected flow path or remain occluded. The local problems were solved on the microstructure obtained from a digitalized micrograph by image analysis. The contribution to macroscopic flow by the soft and dense gels was investigated in various configurations, and comparisons were made with hydraulic conductivity data for MX-80 bentonite.