Carbon Capture and Storage (CCS) is a possible option to mitigate the rise in anthropogenic CO2. When CO2 is injected into a storage formation, it migrates upwards under buoyancy until it reaches the caprock. Of the CO2 that does not dissolve, some may be trapped under the caprock as a free phase and the rest will migrate laterally, which could subsequently cause a risk of CO2 leakage out of a storage complex. Many studies assume a smooth, abrupt interface between the storage and the sealing formations, whereas typically the surface is irregular, due to sedimentological and stratigraphic effects or structural deformation. In this study, the area where the CO2 migrates beneath the caprock is investigated. A set of numerical simulations was conducted to investigate the impacts of various factors on CO2 storage, such as top morphology, tilt and kV/kH, and the presence of a transition zone, where there is a gradational change from storage formation to caprock. These effects were also examined on a realistic field (Lincolnshire Model). It is concluded that a transition zone can increase the security of storage by lessening the amount of CO2 accumulating underneath the caprock. Regarding the top morphology, it is determined that ridges with higher amplitude (larger than the plume thickness) provide more structural trapping if they are perpendicular to the tilt. However, ridges parallel to the tilt provide a pathway for rapid CO2 up dip migration. On the other hand, more CO2 is dissolved due to more migration. Therefore it is important to characterise the interface in terms of the size of irregularities and also in terms of the existence of any transition zone. The latter has not been addressed in previous works. The role of an unconformity at the interface between the caprock and storage formation was also investigated. It is concluded that this can have both positive and negative effects on CO2 storage capacity and security. For example a very thin weathered zone can contribute significantly to pressure diffusion across the model. A novel approach for CO2 injection is presented to minimize vertical migration of CO2 in the storage formation thereby reducing the risk of CO2 leakage. This is achieved by downhole-mixing of CO2 and brine. It is demonstrated that vertical migration of CO2 in the reservoir can be limited due to viscous effects during the injection period, and that during the subsequent shut-in period gravity segregation displaces the CO2 saturated brine downwards, thereby increasing the storage security.