Abstract Tight clay formations are frequently employed as natural or engineered barrier systems in the context of safe disposal of toxic waste. To evaluate long-term barrier efficiency, understanding the spreading and transport of contaminants in these porous media is of critical importance. Tight clay formations exhibit pronounced physical and chemical heterogeneities at various length scales. These heterogeneities potentially dictate the reactive transport characteristics. Modern micro-analytical techniques such as synchrotron-based micro X-ray fluorescence, X-ray spectromicroscopy or X-ray tomographic microscopy, and neutron imaging techniques, as well as laboratory-based microprobe techniques, can be employed to gain new insights into diffusion processes of reactive chemicals occurring in such multi-domain, micro-structured porous media. In addition to structural information, detailed chemical information can be obtained. Most importantly, these modern methods are capable of providing information from within the porous medium directly illustrating the heterogeneous distribution of chemical properties and their inter-relations. Consequently, combined with the capability to image the reactive transport pattern in up to full three dimensions, heterogeneity-reactivity relationships can be derived. Based on the illustrative example of cesium (Cs) migration in Opalinus Clay rock, multi-dimensional and multi-modal imaging of reactive transport phenomena have demonstrated unequivocally that physical and chemical heterogeneities are indeed transport relevant.