Shale caprock integrity is critical in ensuring that subsurface injection and storage of anthropogenic carbon dioxide (CO2) is permanent. The interaction of clay-rich rock with aqueous CO2 under dynamic conditions requires characterization at the nanoscale level due to the low-reactivity of clay minerals. Geochemical mineral–fluid interaction can impact properties of shale rocks primarily through changes in pore geometry/connectivity. The experimental work reported in this paper applied specific analytical techniques in investigating changes in surface/near-surface properties of crushed shale rocks after exposure (by flooding) to CO2–brine for a time frame ranging between 30 days and 92 days at elevated pressure and fractional flow rate. The intrinsically low permeability in shale may be altered by changes in surface properties as the effective permeability of any porous medium is largely a function of its global pore geometry. Diffusive transport of CO2 as well as carbon accounting could be significantly affected over the long term. The estimation of permeability ratio indicated that petrophysical properties of shale caprock can be doubled.