This paper is concerned with the application of a multi-scale model of permeability evolution to the simulation of permeation tests of lead nitrate solutions in a compacted natural bentonite. In a previous work, the weathered hydraulic conductivity has been measured for different pollutant concentrations. Textural and structural evolutions induced by heavy metal sorption have also been investigated, therefore giving us information about the various pore spaces that may be encountered during the process of pollutant leaching. Such knowledge has been exploited during the construction of the numerical microstructures. First of all, pure water permeability tests have been simulated, this has allowed us to ascertain the representation of compacted clay before pollutant permeation. For both Prrenjas and Wyoming clays, permeation tests after pollutant permeation have then been simulated, using connected and non-connected macro-voids configurations. Different conclusions have been drawn based on simulation results for the two different clays investigated, which are supported by experimental evidence.