The long-term geological sequestration of carbon dioxide (CO2) in underground formations (deep saline aquifers) is the most economically viable option to decrease the emissions of this greenhouse gas in the atmosphere. The injection of CO2 in carbonate aquifers dissolves some of the calcite rock due to the formation of carbonic acid as a result of the interaction between CO2 and brine. This rock dissolution may affect the rock integrity and in turn will affect the rock mechanical properties. The effect of CO2 on the rock mechanical properties is a key parameter to be studied to assess the aquifer performance in the process of geological sequestration and to get a safe and effective long-term storage. The main objective of this study is to address the impact of geological sequestration of CO2 on the mechanical properties of carbonate aquifer and caprocks. In addition, the effect of the storage time on these properties is investigated. In this study, CO2 was injected into the brine-soaked core samples under simulated downhole conditions of high pressure and high temperature (2000 psi and 100 °C). The mechanical properties of these core samples were analyzed using indirect tensile strength (ITS), unconfined compression, and acoustics testing machines. The effect of CO2 sequestration on the engineering operations such as well instability and aquifer compaction will be investigated based on the experimental results. Results showed that CO2 sequestration affected the mechanical properties of the carbonate rocks as well as the caprocks. Long time soaking of CO2 in brine allowed for the formation of enough carbonic acid to react with the cores and this greatly impacted the rock mechanical and acoustic properties. The significant impact of CO2 storage was noted on Khuff limestone (KL), and the good candidate among the carbonate rocks studied here for geological sequestration of CO2 is found to be Indiana limestone (IL). The stress calculations based on the experimental results showed that CO2 may affect the wellbore stability and care should be taken during drilling new wells in the sequestration area. Aquifer compaction based on KL measurements showed that the aquifer will compact 1.25 ft for a 500 ft thick carbonate formation due the CO2 sequestration for 90 days.