Although there are a number of mathematical modeling studies for carbon dioxide (CO2) injection into aquifer formations, experimental studies are limited and most studies focus on injection into sandstone reservoirs as opposed to carbonate ones. This study presents the results of computerized tomography (CT) monitored laboratory experiments to analyze permeability and porosity changes as well as to characterize relevant chemical reactions associated with injection and storage of CO2 in carbonate formations. CT monitored experiments are designed to model fast near well bore flow and slow reservoir flows. Highly heterogeneous cores drilled from a carbonate aquifer formation located in South East Turkey were used during the experiments. Porosity changes along the core plugs and the corresponding permeability changes are reported for different CO2 injection rates and different salt concentrations of formation water. It was observed that either a permeability increase or a permeability reduction can be obtained. The trend of change in rock properties is very case dependent because it is related to distribution of pores, brine composition and thermodynamic conditions. As the salt concentration decreases, porosity and the permeability decreases are less pronounced. Calcite deposition is mainly influenced by orientation, with horizontal flow resulting in larger calcite deposition compared to vertical flow.