Performance assessment of nuclear waste repositories requires state-of-the-art knowledge of radionuclide transport properties. Additionally, the short-term development under thermal pulses and the long-term development of the near field—due to influences such as gas generation—must be evaluated. Key thermal-hydro-mechanical-chemical processes are strongly coupled on different spatial and temporal scales. To understand these coupling mechanisms, numerous material models and numerical codes have been developed. However, the existing constitutive approaches—which have been adapted to describe small-scale laboratory experiments and validated against real-scale field observations—are often unable to capture long-term material behavior with sufficient precision. To build the confidence, a more comprehensive understanding of the system at micro- and macroscopic scales is required. Most observed macroscopic processes result from microscopic changes in the crystal structure and/or crystalline aggregates, as well as changes in material properties under the influence of various factors. To characterize these physical fields in crystals, microscopic investigations, such as visualization, or geophysical methods are introduced to verify the understanding at the microscale. Two cases are demonstrated for the presented concept using microscale information: one deals with the mechanically and thermally driven migration of fluid inclusions in rock salt, the other with dilatancy-controlled gas transport in water-saturated clay material.