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Potential CO2 leakage from deep geologic reservoirs requires evaluation on a site-specific basis to assess risk and arrange mitigation strategies. In this study, a heterogeneous and realistic numerical model was developed to investigate CO2 migration pathways and uprising time in a shaly overburden, located in the Malaysian off-shore. Fluid flow and reactive transport simulations were performed by TOUGHREACT to evaluate the: (1) seepage through the caprock; (2) CO2-rich brine leakage through a fault connecting the reservoir with seabed. The effect of several factors, which may contribute to CO2 migration, including different rock types and permeability, Fickian and Knudsen diffusion and CO2 adsorption in the shales were investigated. Obtained results show that permeability mainly ruled CO2 uprising velocity and pathways. CO2 migrates upward by buoyancy without any important lateral leakages due to poor-connection of permeable layers and comparable values of vertical and horizontal permeability. Diffusive flux and the Knudsen flow are negligible with respect to the Darcy regime, despite the presence of shales. Main geochemical reactions deal with carbonate and pyrite weathering which easily reach saturation due to low permeability and allowing for re-precipitation as secondary phases. CO2 adsorption on shales together with dissolved CO2 constituted the main trapping mechanisms, although the former represents likely an overestimation due to estimated thermodynamic parameters. Developed models for both scenarios are validated by the good agreement with the pressure profiles recorded in the exploration wells and the seismic data along a fault (the F05 fault), suggesting that they can accurately reproduce the main processes occurring in the system. [ABSTRACT FROM AUTHOR]