CO2 sequestration and injection projects are being intensively studied and conducted throughout the world. The CO2 has to be trapped below a caprock and the trap itself occurs in a complex geological setting which creates a complex geometrical model. Increased pore pressure may result in uplift of the formation and generation of new fractures or reactivation of existing structures that will generate preferred fluid flow pathways along which dissolved CO2 which may escape into the atmosphere or freshwater zones above, or result in seismicity in the region. In order to assess and mitigate these geomechanical risks, a thorough simulation coupling fluid flow through porous media and geomechanics of a realistic representation of the reservoir as well as the overburden is required. Many aspects of geomechanics and reservoir simulation coupling has been studied using idealized horizontal layer basin structures that share the same discretization of the reservoir for the two simulators, and few modeling studies of real reservoirs are carried out, but limited effort has been made for mitigating the fractures forming at the cap rock in a real reservoir. The shared earth model of a candidate shallow CO2 sequestration site in the state of Missouri was separately discretized before coupled simulation in the finite element software and reservoir simulator predicted fracture formations. A coupling module was developed which uses the relative spatial position of Finite Element nodes compared to Finite Difference grid blocks to relate the two simulation grids. Fluid flow properties such as reservoir pressure and fluid saturations are taken from the reservoir simulation and are fed into the finite element simulation model, from which a new state of stress together with new porosities and pseudo compressibility values are calculated and are used to update the reservoir model. Results of this study are used for predicting the best CO2 injection location and injection rates to provide maximum storage capacity and injection rates for safe sequestration. This approach also predicts the critical pore pressures which result in formation of extensional or shear fractures at different places in caprock. This knowledge is then used for determining type, time and amount of sealant to inject for mitigation of flow through caprock fractures so that storage of CO2 at required injection rate is maintained.