Knowing the structure of a material is necessary to understand its evolution under various influences; here, the alteration by water of a reference glass of nuclear interest, called International Simple Glass (ISG), is studied. The ISG atomic structure has not yet been thoroughly characterized. Short- and medium-range order in this six-oxide glass was investigated by molecular dynamics (MD) methods. Combining the simulated data with experimental observations acquired from both pristine and altered ISG provided new insight into the formation of surface layers and passivation of the underlying glass. In the tested conditions of 90 °C, silica-saturated solution, and pH90°C 7, the passivating layer partly inherits the structure of the pristine glass network despite the release of mobile elements (Na, B, and some Ca), with a reorganization of the silicate network following B release. The layer appears to minimize its internal energy by relaxing strain accumulated during glass quenching. The resulting passivated glass shows a strong resistance to hydrolysis. The nanopores of this hydrated material, displaying a mean pore size of ∼1 nm, are filled with various water species. Water speciation determination inside the nanopores is therefore an achievement for future water dynamic study in the passivated glass.