An unusual highly hydrated and Na-depleted variety of elpidite was identified in a hydrothermally altered peralkaline pegmatite at Mt. Yukspor in the Khibiny alkaline complex, Kola Peninsula, Russia. It differs from ‘ordinary’ elpidite, ideally Na2ZrSi6O15⋅3H2O, in its crystal chemical features, infrared spectrum and optical characteristics. The chemical composition (wt.%, electron microprobe, H2O by TGA) is: Na2O 5.45, K2O 0.67, CaO 0.05, SiO2 60.32, TiO2 1.34, ZrO2 18.43, Nb2O5 0.65, H2O 12.80, total 99.71. The empirical formula calculated on the basis of 6 Si and 15 O atoms is [(Na1.05K0.08Ca0.01)Σ1.14(H3O)0.74]Σ1.88(Zr0.89Ti0.10Nb0.03)Σ1.02Si6O15⋅3.47H2O; the H2O:H3O ratio was calculated from the charge balance requirement, taking into account the results of crystal structure refinement. The highly hydrated variety of elpidite is orthorhombic, Pma2, a = 14.5916(6), b = 7.3294(3), c = 7.1387(2) Å, V = 763.47(5) Å3 and Z = 2. The crystal structure was solved from single-crystal X-ray diffraction data, R1 = 3.43%. The structure is based upon an elpidite-type heteropolyhedral Zr–Si–O framework with Na+ and H3O+ cations and H2O molecules in the zeolitic channels. Hydronium cations substitute for water molecules in one of the extra-framework sites. This variety of elpidite could be considered as an intermediate product of natural ion-exchange reaction between ‘ordinary’ elpidite and a low-temperature hydrothermal fluid.