We investigate a prototypical reaction–diffusion-flow problem in saturated/unsaturated porous media. The special features of our problem are twofold: the reaction produces water and therefore the flow and transport are coupled in both directions and moreover, the reaction may alter the microstructure. This means we have a variable porosity in our model. For the spatial discretization we propose a mass conservative scheme based on the mixed finite element method (MFEM). The scheme is semi-implicit in time. Error estimates are obtained for some particular cases. We apply our finite element methodology for the case of concrete carbonation—one of the most important physico-chemical processes affecting the durability of concrete.