The paper addresses the issues of reducing the concentration of greenhouse gases in the atmosphere through carbon dioxide sequestration by injection to geological formations to enhance oil recovery and underground storage. Geochemical reactions occurring in a reservoir during CO2 injection can affect physical properties of the formation and mechanisms of carbon dioxide capture. The interactions in the “CO2-formation water-rock” system are complex and depends on many factors: mineralogical composition of rock, composition and salinity of formation water, reservoir thermobaric conditions, time. The paper includes a brief review of carbon dioxide interaction studies with formation fluids and reservoir rock minerals. A methodology is presented for studying geochemical processes during interaction of carbon dioxide-saturated formation water with reservoir rock samples. Experimental results for oil-saturated and water-saturated, carbonate and terrigenous reservoir intervals are discussed. The experiments demonstrate complex interactions of CO2 with water and rocks under natural conditions. Important aspects are the influence of mineralogical composition on dissolution and secondary precipitation processes as well as changes in aqueous phase composition and pH. Hydrogeochemical modeling workflow for the studied processes is proposed with calibration to experimental data and their appropriate translation to reservoir conditions. The results demonstrate the need for detailed geochemical studies to better assess the effects of CO2 on reservoir properties and the risks associated with mineral deposition and dissolution during carbon capture and storage (CCS/CCUS) operations.