The structural behavior of thomsonite compressed in aqueous medium up to 3 GPa was studied by means of in situ synchrotron powder diffraction with a diamond anvil cell. In the range between 0.0001 and 2 GPa, the compressibility of thomsonite is markedly lower than that reported previously, where a non-penetrating medium (with only 6% H2O) was used. This indicates a pressure-induced hydration (PIH), which results in the transition to an over-hydrated phase observed at 2 GPa. The structure of over-hydrated thomsonite contains one additional, half-occupied H2O position, coordinated by the calcium at the Ca2 site, with a scolecite-like coordination [CaO4(H2O)3]. The appearance of new H2O position causes a 4.5% volume expansion through the cooperative rotation of [T2O5]∞ chains, leading to the enlargement of the cross-section of the main channels parallel to c axis. The observed deformation mechanism is similar to that found in high-hydrated and super-hydrated natrolite, although only a half of the channels are affected by PIH. The present data indicate that the over-hydration effect in fibrous zeolites strongly depends on the partial water pressure in compressing medium.