To study the alteration of Portland cement mortar from the El Cabril disposal facility under advective water flow conditions, and to test the applicability of the C–S–H dissolution rate law obtained in our previous study, experiments using columns filled with mortar fragments were performed. Variation of the chemical composition of the output solutions and the analyses of the mortar fragments by means of visual inspection, SEM and X-ray fluorescence (XRF), before and after the experiments, allowed interpretation of the dissolution and precipitation reactions by means of two-dimensional reactive transport calculations. The 2D model included an immobile zone (mortar grains) and a mobile zone (flowing water). The reactive transport model adequately reproduced the processes of portlandite dissolution and C–S–H dissolution and decalcification. The results proved the applicability of the previously obtained dissolution rate law of the C–S–H gel, although some uncertainties remain.