One of the most promising means of reducing carbon content in the atmosphere, which is aimed at tackling the threats of global warming, is injecting carbon dioxide (CO2) into deep saline aquifers (DSAs). Keeping this in mind, this research aims to investigate the effects of various injection schemes/scenarios and aquifer characteristics with a particular view to enhance the current understanding of the key permanent sequestration mechanisms, namely, residual and solubility trapping of CO2. The paper also aims to study the influence of different injection scenarios and flow conditions on the CO2 storage capacity and efficiency of DSAs. Furthermore, a specific term of the permanent capacity and efficiency factor of CO2 immobilization in sedimentary formations is introduced to help facilitate the above analysis. Analyses for the effects of various injection schemes/scenarios and aquifer characteristics on enhancing the key permanent sequestration mechanisms is examined through a series of numerical simulations employed on 3D homogeneous and heterogeneous aquifers based on the geological settings for Sleipner Vest Field, which is located in the Norwegian part of the North Sea. The simulation results highlight the effects of heterogeneity, permeability isotropy, injection orientation and methodology, and domain-grid refinement on the capillary pressure–saturation relationships and the amounts of integrated CO2 throughout the timeline of the simulation via different trapping mechanisms (solubility, residual and structural) and accordingly affect the efficiency of CO2 sequestration. The results have shown that heterogeneity increases the residual trapping of CO2, while homogeneous formations promote more CO2 dissolution because fluid flows faster in homogeneous porous media, inducing more contact with fresh brine, leading to higher dissolution rates of CO2 compared to those in heterogeneous porous medium, which limits fluid seepage. Cyclic injection has been shown to have more influence on heterogenous domains as it increases the capillary pressure, which forces more CO2 into smaller-sized pores to be trapped and exposed to dissolution in the brine at later stages of storage. Storage efficiency increases proportionally with the vertical-to-horizontal permeability ratio of geological formations because higher ratios facilitate the further extent of the gas plume and increases the solubility trapping of the integrated gas. The developed methodology and the presented results are expected to play key roles in providing further insights for assessing the feasibility of various geological formations for CO2 storage.