Deuterated BaTi0.5In0.5O2.75 has been studied with neutron total (Bragg plus diffuse) scattering data, using both the Rietveld refinement method and the reverse Monte Carlo (RMC) modelling technique, to investigate the preferred proton site and its local structural environment. The Rietveld analysis shows an excellent fit between experimental data and a long-range cubic description of the BaTi0.5In0.5O2.53(OD)0.44 perovskite structure containing a statistical distribution of Ti and In ions at the centre of regular (Ti/In)O6 octahedra. However, an RMC analysis of the data reveals substantial local structural features that reflect limitations of the Rietveld method for studies of this type. The Ti-O and In-O pair distribution functions given by the RMC analysis are markedly different from each other, with average Ti-O and In-O bond distances of 2.035 Å and 2.159 Å, respectively. The InO6 octahedra are regular in shape whereas the TiO6 octahedra are distorted. The average O-D bond distance is roughly 0.96 Å, and the preferred deuteron sites have a second nearest oxygen distance of 2.13 Å, which confirms localized tilting of the deuteron and indicates a substantial degree of hydrogen bonding. The impact of octahedral distortion and hydrogen bonding on the proton conduction mechanism is discussed.