There have been many studies carried out in the past decade to evaluate the long-term integrity of seals in CO₂ storage sites. These seals (caprock and faults) are often dominated by shale and may act as a capillary barrier against the CO₂ migration. Thus, geochemical reactions, mineral transformations, surface wettability alteration and reduction of capillary pressure that may take place in a geological storage site must be deeply understood. The main objective of this study is to examine the changes in the mineralogy and surface wettability of shales with different clay contents once exposed to supercritical CO₂ for 6 months. The results obtained indicated that quartz dissolution and kaolinite precipitation can be induced in the presence of supercritical CO₂. It appeared that brine in a concentration less than 4000 ppm could help to maintain the water wettability of the clay surface. Changes of surface wettability in a storage site could be a dynamic process and linked to the reduction of the surface areas in clays and their affinity to absorb CO₂. Given that the interactions between CO₂ and rocks are very slow and may take place over a long period of time, further studies are needed to ensure the integrity of seals in storage sites during and after injection.