As one of the solutions to tackle climate change caused by excess carbon dioxide (CO2) emission, CO2 geological storage has been increasingly implemented globally to store CO2 securely and permanently in the subsurface. In the current study, structural trapping, which shows the potential of initial CO2 containment and integrity of the subsurface structure, is experimentally investigated with CO2 leakage assessed. CO2 containment is quantified by CO2 column height, which describes the amount of CO2 accumulated in the formation underneath seal rock and is controlled by a balance between capillary and gravitational forces acting on formation brine and invading CO2. While previous studies considered only contributions from seal rock (i.e., “nonrelative”), the current study examines a concurrent contribution from reservoir rock as a seal–reservoir “relative” column height since CO2 storage as an analogy to petroleum reservoir is a structural trap consisting of the reservoir and impermeable seal covered. A distinctive discrepancy was found between the resultant relative and nonrelative column heights. The nonrelative column heights were positive (∼3000 m), implying a high potential for CO2 storage. On the contrary, with reservoir rock contribution considered, the relative column heights were negative (∼−1800 m), suggesting CO2 leakage through the structural trap. This was attributed to a relatively larger reservoir pore size (5.72 nm) than that of seal rock (4.04 nm). Hence, the contribution from reservoir rock characteristics is non-negligible when analyzing CO2 storage potential. Owing to CO2 dissolution in formation brine, CO2-induced effects including a geochemical reaction between acidic carbonated brine and rocks were also investigated. Rock dissolutions in both seal (claystone) and reservoir (limestone) rocks were observed with changes in the pore size, leading to lower storage potential. Further attempts to improve the column height were made by hydrophobizing seal rock via surfactant adsorption, although the changes were slight and could only facilitate a possible leakage (less negative height column).