The future emissions of carbon dioxide (CO2) are likely to increase beyond the current levels due to rapid industrialization in China. Several methods have been proposed as possible mitigation strategies to reduce the anthropogenically emitted CO2 from the atmosphere and water. This study provided the description of stratigraphic structure of the basin through analysis between the regional groundwater flow and the injection of carbon dioxide. The geological and geomechanical data was used to model the aquifer for geostatistical analysis. Data storage sites for geotechnical provided critical information to assess the potential risks and associated sequestration. The movement of groundwater occurred slowly with infiltration through the pores. CO2 was stored in deep aquifers for longer periods due to slow movement of water downstream. Over time, the injected CO2 dissolved water, forming minerals through chemical reactions, which converted it into carbonate minerals resulting in permanent sequestration. The chemistry of formation waters in this basin is important for many geological processes, such as the fluid-rock interaction, the migrating paths of fluid and the entrapment mechanisms of hydrocarbon. In this study, the emissions of CO2 were shifted several kilometers away from the storage area, such that the regional groundwater mixing affected the quality of surface water with consequent of toxicity to every living creature that depended on the available water from Urumqi River Basin. Injection of fluids into deep saline aquifers is therefore considered as the best mitigating strategy for CO2 abatement in water due to its enormous storage capacity.