Temperature-dependent total X-ray scattering measurements for water confined in bioactive glass samples with 5.9 nm pore diameter have been performed. Based on these experimental data, simulations were carried out using the Empirical Potential Structure Refinement ( EPSR ) code, in order to study the structural organization of the confined water in detail. The results indicate a non-homogeneous structure for water inside the pore, with three different structural organizations of water, depending on the distance from the pore surface: (i) a first layer (4 Å) of interfacial pore water that forms a strong chemical bond with the substrate, (ii) intermediate pore water forming a second layer (4–11 Å) on top of the interfacial pore water, (iii) bulk-like pore water in the centre of the pores. Analysis of the simulated site–site partial pair distribution function shows that the water–silica (O w –Si) pair correlations occur at ∼3.75 Å. The tetrahedral network of bulk water with oxygen–oxygen (O w –O w ) hydrogen-bonded pair correlations at ∼2.8, ∼4.1 and ∼4.5 Å is strongly distorted for the interfacial pore water while the second neighbour pair correlations are observed at ∼4.0 and ∼4.9 Å. For the interfacial pore water, an additional O w –O w pair correlation appears at ∼3.3 Å, which is likely caused by distortions due to the interactions of the water molecules with the silica at the pore surface.