Most sedimentary rock formations (tight or highly porous) have geochemical characteristics that can lead to significant reactive ion exchange processes in aqueous media in the presence of carbondioxide. While geomechanical properties such as rock stiffness, Poisson’s ratio and fracture geometry largely govern fluid flow characteristics in deep fractured formations, the effect of mineralization can lead to flow impedance in the presence of favorable geochemical and thermodynamic conditions. Shale caprock which seals more than 60% of oil and gas reservoirs have natural fractures that are unevenly distributed in the geosystem. Experimental works which employed the use of analytical techniques such ICP-OES, XRD, and SEM/EDS techniques in investigating diagenetic and micro-structural property of crushed shale caprock/CO2-brine system concluded that net precipitation reaction processes can affect the distribution of petrophysical nanopores in the seal rock. The results showed that geochemical precipitates can be formed such that fluid flow through open micro and macro fractures may be constrained. Simulation results reported by various researchers suggested that influx-induced mineral dissolution/precipitation reactions within shale caprocks can continuously close micro-fracture networks, while pressure and effective-stress transformation first rapidly expand then progressively constrict them. This experimental research investigates the impact of in-situ geochemical precipitation on conductivity of open micro-fractures under geomechanical stress conditions. Fracture conductivity in core samples of shale caprock with known mineralogical composition from different formations where CO2 injection is on-going are quantitatively evaluated under axial and radial stress using pressure pulse-decay liquid permeametry/core flooding systems. Modeling of the diffusion controlled fluid flow and induced fracture diagenetic alterations in the shale caprocks can be performed using CMG-GEM with artificial core imposing axial and radial geomechanical stress. The possibility of rock-fluid geochemical interactions constricting natural fracture conductivity in long term subsurface CO2 sequestration can lead to significant improvement in shale caprock seal integrity and mitigate injection induced geomechanical perturbation.