The photocatalytic activity of layered perovskite-like oxides in water splitting reaction is dependent on the hydration level and species located in the interlayer slab: simple or complex cations as well as hydrogen-bonded or non-hydrogen-bonded H2O. To study proton localization and dynamics in the HCa2Nb3O10·yH2O photocatalyst with different hydration levels (hydrated—α-form, dehydrated—γ-form, and intermediate—β-form), complementary Nuclear Magnetic Resonance (NMR) techniques were applied. 1H Magic Angle Spinning NMR evidences the presence of different proton containing species in the interlayer slab depending on the hydration level. For α-form, HCa2Nb3O10·1.6H2O, 1H MAS NMR spectra reveal H3O+. Its molecular motion parameters were determined from 1H spin-lattice relaxation time in the rotating frame (T1ρ) using the Kohlrausch-Williams-Watts (KWW) correlation function with stretching exponent β = 0.28: Ea=0.210(2) eV, τ0=9.0(1) × 10−12 s. For the β-form, HCa2Nb3O10·0.8H2O, the only 1H NMR line is the result of an exchange between lattice and non-hydrogen-bonded water protons. T1ρ(1/T) indicates the presence of two characteristic points (224 and 176 K), at which proton dynamics change. The γ-form, HCa2Nb3O10·0.1H2O, contains bulk water and interlayer H+ in regular sites. 1H NMR spectra suggest two inequivalent cation positions. The parameters of the proton motion, found within the KWW model, are as follows: Ea=0.217(8) eV, τ0=8.2(9) × 10−10 s.