CO$_2$ sequestration in subsurface reservoirs is important for limiting atmospheric CO$_2$ concentrations. However, a complete physical picture able to predict the structure developing within the porous medium is lacking. We investigate theoretically reactive transport in the long-time evolution of carbon in the brine-rock environment. As CO$_2$ is injected into a brine-rock environment, a carbonate-rich region is created amid brine. Within the carbonate-rich region minerals dissolve and migrate from regions of high concentration to low concentration, along with other dissolved carbonate species. This causes mineral precipitation at the interface between the two regions. We argue that precipitation in a small layer reduces diffusivity, and eventually causes mechanical trapping of the CO$_2$. Consequently, only a small fraction of the CO$_2$ is converted to solid mineral; the remainder either dissolves in water or is trapped in its original form. We also study the case of a pure CO$_2$ bubble surrounded by brine and suggest a mechanism that may lead to a carbonate-encrusted bubble due to structural diffusion.