This paper reports on the one‐pot synthesis and characterization of the functionalized mesoporous SBA‐15 silica, which contains two loadings of the different acid groups [CO2H, PO(OH)2 and SO3H]. The thermodynamic features of the water that was confined in these porous silicas was investigated by Differential Scanning Calorimetry (DSC). The results showed that the melting behaviour of the confined water was mainly governed by the pore diameter and, as a consequence, indicated that the chemical “decoration” of the porous surface did not play a key role in the water thermodynamics. On the contrary, the proton conductivity of the hydrated mesoporous materials, which was examined under a wide range of temperatures (–100 to 70 °C), was strongly dependent on both the physical state of the confined water and the acidity of the functional groups that were located at the porous surface. The proton conductivity was shown to be directly related to the pKa and the density of the functional groups attached to the mesopore surface. The high conductivity values that were obtained at a low temperature when the confined water is frozen, led us to postulate that the SO3H‐functionalized SBA‐15 sample could be a promising candidate for electrolyte solid applications in fuel cells.