In previous work, the impact of lithological variations on the transport properties of the Boom Clay and EigenbiIzen Sands and their correlation was studied. However, some questions such as understanding the variability of the geometric factor with the size of the diffusing molecule remain. Therefore, linking transport properties to the microstructure was an essential step in solving remaining questions. A detailed petrographical study, including medical CT, micro-CT and light microscopy of thin sections was performed on the same sample set. Results indicated clear differences in the microstructure of the Boom Clay and Eigenbilzen Sands. Boom Clay samples were dominated by a clay matrix with a homogeneous distribution of quartz grains. Pores were small and mainly located in the clay matrix. In contrast, samples of the Eigenbilzen Sands showed large amounts of quartz, heterogeneous distribution of the clay phase and interparticle porosity between quartz grains. Porosity was mainly located in between the quartz grains, only a small fraction was located in the clay matrix. Larger pores could be linked to increased hydraulic conductivity and diffusivity of dissolved gases in samples of the Eigenbilzen Sands. Results of CT, micro-CT and light microscopy were complementary and provided a global view on the pore structure, supported by the pore size distribution derived from N2-desorption and MIP measurements.