The crystal structure of deuterated natrolite, Na1.85Mg0.05Ca0.03[Al2.06Si 2.95O10]·nD2O, compressed in liquid D2O at 0.9 and 1.0 GPa has been determined from neutron powder diffraction data. At 0.9 GPa, the crystal structure is close to the original natrolite with the same space group Fdd2 and 1 % smaller unit cell volume. New water positions are found in addition to the original ones indicating the early stage of natrolite over-hydration. The unit cell volume of high-pressure phase stable at 1.0 GPa is expanded by 5.4 % with respect to initial natrolite. According to structural investigations, HP phase contains 3.5 water molecules pfu. Higher degree of hydration is accompanied by the drastic rearrangement of extra-framework subsystem, water molecules occupying four independent positions. Three of them belong to Na+ coordination sphere and together with three framework O-atoms form a distorted octahedron. Water molecule in the fourth position (occupancy = 0.5) has no contact to the cations. The evolution of natrolite structure with increasing pressure is discussed in terms of framework flexibility and hydrogen bonding rearrangement.