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The lithium-argyrodites Li6PS5X (X = Cl, Br, I) exhibit high lithium-ion conductivities, making them promising candidates for use in solid-state batteries. These solid electrolytes can show considerable substitutional X−/S2− anion-disorder, with greater disorder typically correlated with higher lithium-ion conductivities. The atomic-scale effects of this anion site-disorder within the host lattice—in particular how lattice disorder modulates the lithium substructure—are not well understood. Here, we characterize the lithium substructure in Li6PS5X (X = Cl, Br, I) as a function of temperature and anion site-disorder, using Rietveld refinements against temperature-dependent neutron diffraction data. Analysis of these high-resolution diffraction data reveals an additional lithium position previously unreported for Li6PS5Xargyrodites, suggesting that the lithium conduction pathway in these materials differs from the most common model proposed in earlier studies. Analysis of the Li+ positions and their radial distributions reveals that greater inhomogeneityof the local anionic charge, due to X−/S2− site-disorder, is associated with more spatially-diffuse lithium distributions. This observed coupling of site-disorder and lithium distribution provides a possible explanation for the enhanced lithium transport in anion-disordered lithium argyrodites, and highlights the complex interplay between anion configuration and lithium substructure in this family of superionic conductors.