To guarantee the durability of new cement and concrete formulations, we need to understand the long-term degradation mechanisms and how they relate to the evolution of the microstructure. Inside a porous medium, the different phenomena are coupled by the microstructure and its evolution. For example, in coupled simulation of drying and carbonation, the entry of CO2 and release of water will occur through the carbonated layer which has distinct properties from the non-carbonated core. To solve this problem, we propose a new reactive transport implementation which can integrate a custom-made microstructure model adapted to the problem at hand. This feature has many strong numerical challenges and it leads to a robust and flexible reactive transport framework. We demonstrate its capabilities through coupled carbonation and drying simulation of cement pastes. We show that the water transport properties are key elements in the rate of propagation of the carbonation reaction. To reach quantitative prediction abilities, the capillary pressure and the relative transport properties must be computed accurately in both the carbonated and the non-carbonated layers.