ABSTRACT The structural properties of water confined in two silica matrices characterised by well-controlled organised porosity with a narrow pore size distribution: i) a new mesoporous bioactive glass (MBG 92S6) and ii) SiO2 MCM-41 were studied using laboratory total X-ray scattering coupled to molecular pair distribution function (PDF). The PDF analysis shows that the hydrophilic/hydrophobic character of the water-bioglass interface affects the structural properties of the confined water in the same way as water confined in different mesoporous matrices presenting an intermediate hydrophilic and hydrophobic interface regardless of their pore size and distribution. We also compare the effect of the confinement inside MBG 92S6 and different mesoporous hydrophilic and hydrophobic silica matrices. We show that the pore surface properties have a stronger influence on the structural organisation of the confined water than the pore size distribution.