The long-term exposure of rocks to supercritical carbon dioxide (scCO2) during sequestration creates structural and chemical changes. In turn, these lead to changes in the permeability of inter-layers and caprocks that can alter plume migration behaviour and/or lead to the loss of the sealing efficiency of caprocks. This review first surveys experimental studies of changes to the pore structure and mass transport properties of caprocks and interlayers, including novel experimental protocols and data analysis methods. These methods provide more accurate measures of basic parameters, such as surface area, as well as new information on pore network features that are essential to properly understanding changes to mass transport properties. The subsequent evolution of rocks exposed to scCO2 involves a complex coupling of geomechanics, geochemistry, and mass transport processes over different length and time scales. The simultaneous combination of all three factors together is rarely considered and this review also surveys such fully integrated work to understand the complex interplay and feedback arising between the different processes. We found that it was necessary to include all three coupled processes to obtain truly representative behaviour in reservoir simulations; otherwise, counter-intuitive effects are missed. These include the unexpected greater sealing efficiency of thin shale layers.