The components of a fluid mixture may segregate due to the Soret effect, a coupling phenomenon in which mass flux can be induced by a thermal gradient. In this work, we evaluate systematically the thermodiffusion of the CO 2 −H 2 O mixture, and the influence of the geothermal gradient on CO 2 segregation in deep saline aquifers in CO 2 storage. The eHeX method, a nonequilibrium molecular dynamics simulation approach, is judiciously selected to simulate the phenomenon. At 350 K, 400 bar, and CO 2 mole fraction of 0.02 (aquifer conditions), CO 2 accumulates on the cold side, and the thermal diffusion factor is close to 1 in a number of force fields. The lower the temperature, the higher is the separation and the thermal diffusion factor. In colder regions, water self-association is stronger, whereas the CO 2 −H 2 O cross-association and the CO 2 −CO 2 interactions enhance at higher temperatures. Thermodiffusion and gravitational segregation have opposite effects on CO 2 segregation. At typical subsurface conditions, the Soret effect is more pronounced than gravity segregation, and CO 2 concentrates in the top (colder region). Our work sets the stage to model the effect of electrolytes on CO 2 segregation in subsurface aquifers and other areas of interest.