In a previous work, a multi-scale model has been developed in order to investigate the impact of cation exchange and surface complexation on the hydraulic conductivity of two contrasted compacted bentonites. Hydraulic conductivity variations during the percolation of a lead nitrate solution have been simulated using occluded and connected inter-aggregate void configurations. For both clays, the results have displayed the strong connection between permeability increase and textural and structural evolutions at different scales during the process of pollutant leaching. The present developments deal with the modelling of pollutant transport through compacted bentonite, by accounting for advective transport, molecular diffusion within the nanoscale interlayer pores and the inter-aggregate macro-voids, as well as pollutant fixation on the smectite layers' surface. The evolution of the different porous spaces is modelled on the basis of an extensive structural investigation of the solid phase conducted at the nanometer and micrometer scales. The multi-scale impact of ionic exchange by heavy metal on macroscopic pollutant transport is expressed through upscaling at the different scales of organization within the compacted clay. We compare the respective contributions of hydraulic conductivity , effective diffusion and pollutant uptake to the overall pollutant transport during progressive reduction of the interlamellar space associated with clay aggregate splitting and the development of inter-aggregate pores. Lead nitrate percolation tests are simulated for a reference bentonite and a natural magnesian bentonite. Keywords multi-scale transport model · interlamellar and inter-aggregate pores · effective diffusion tensor · effective hydraulic conductivity tensor · finite element simulation · breakthrough curves