Perovskite-based material Sc-doped BaZrO₃ is a promising protonic conductor but with substantially lower conductivities than its Y-doped counterpart. ¹H solid-state NMR spectroscopy in combination with DFT modelling was used to analyze the protonic distribution in BaZr_1−xSc_xO_3−x/2−y(OH)_2y and its effect on charge carrier mobility. ¹H single pulse and ¹H–⁴⁵Sc TRAPDOR MAS NMR experiments highlighted the mobile character of the proton charge carriers at room temperature, giving rise to a single broad resonance, protons hopping between multiple sites on the NMR timescale. At low temperatures, the protonic motion was successfully slowed down allowing direct observation of the various proton environments present in the structure. For x ≤ 0.15, DFT modelling suggested a tendency for strong dopant–proton association leading to Sc–OH–Zr environments with ¹H NMR shifts of 4.8 ppm. The Zr–OH–Zr environment, H-bonded to a Sc–O–Zr, lies 32 kJ mol⁻¹ higher in energy than the Sc–OH–Zr environment, suggesting that the Sc–OH–Zr environment is trapped. However, even at these low concentrations, Sc–Sc clustering could not be ruled out as additional proton environments with stronger ¹H–⁴⁵Sc dipolar couplings were observed (at 4.2 and 2.8 ppm). For x = 0.25, DFT modelling on the dry material predicted that Sc-□-Sc environments were extremely stable, again highlighting the likelihood of dopant clustering. A large number of possible configurations exists in the hydrated material, giving rise to a large distribution in ¹H chemical shifts and multiple conduction pathways. The ¹H shift was found to be strongly related to the length of the O–H bond and, in turn, to the hydrogen bonding and O⋯OH distances. The breadth of the NMR signal observed at low temperature for x = 0.30 indicated a large range of different OH environments, those with lower shifts being generally closer to more than one Sc dopant. Lower DFT energy structures were generally associated with weaker H-bonding environments. Both the calculations and the DFT modelling indicated that the protons tend to strongly bond to the Sc clusters, which, in conjunction with the higher energies of configurations containing Zr–OH–Zr groups, could help explain the lower conductivities recorded for the Sc-substituted BaZrO₃ in comparison to its yttrium counterpart.