Of all the strategies to reduce carbon emissions, carbon dioxide (CO₂) geological sequestration is an immediately available option for removing large amounts of the gas from the atmosphere. However, our understanding of the transition behavior between Forchheimer and Darcy flow through porous media during CO₂ injection is currently very limited. In addition, the kinetic mass transfer of SO₂ and CO₂ from CO₂ stream to the saline and the fully coupling between the changes of porosity and permeability and multiphase flow are two significant dimensions to investigate the brine acidification and the induced porosity and permeability changes due to SO₂ co-injection with CO₂. Therefore, this dissertation develops a multiphase flow, contaminant transport and geochemical model which includes the kinetic mass transfer of SO₂ into deep saline aquifers and obtains the critical Forchheimer number for both water and CO₂ by using the experimental data in the literature. The critical Forchheimer numbers and the multiphase flow model are first applied to analyze the application problem involving the injection of CO₂ into deep saline aquifers. The results show that the Forchheimer effect would result in higher displacement efficiency with a magnitude of more than 50% in the Forchheimer regime than that for Darcy flow, which could increase the storage capacity for the same injection rate and volume of a site. Another merit for the incorporation of Forchheimer effect is that more CO₂ would be accumulated in the lower half of the domain and lower pressure would be imposed on the lower boundary of the cap-rock. However, as a price for the advantages mentioned above, the injection pressure required in Forchheimer flow would be higher than that for Darcy flow. The fluid flow and contaminant transport and geochemical model is then applied to analyze the brine acidification and induced porosity and permeability changes due to SO₂ co-injection. The results show that the co-injection of SO₂ with CO₂ would lead to a substantially acid zone near the injecting well and it is important to include the kinetic dissolution of SO₂ from the CO₂ stream to the water phase into the simulation models, otherwise considerable errors would be introduced for the equilibrium assumption. This study provides a useful tool for future analysis and comprehension of multiphase Darcy-Forchheimer flow and brine acidification of CO₂ injection into deep saline aquifers. Results from this dissertation have practical use for scientists and engineers concerned with the description of flow behavior, and transport and fate of SO₂ during SO₂ co-injection with CO₂ in deep saline aquifers.