Relationships between the surface chemistry, particle morphology, and “internal” crystal structure in the polymorph-rich family of layered MnO2 (Birnessite or Chalcophanite) have strong implications on terrestrial recycling, and critically influence the abilities of catalytically and electrochemically active variants. Intense research and development efforts are aimed at characterizing and optimizing the interfaces of such nanostructured materials, yet the identity, concentration, and structure of surface species and their influence on underlying structures are often ambiguous: the availability of experimental tools to observe atomic level details in relevent environmental/operating conditions remains limited. We present our investigation of the local and long-range structure of synthetic layered δ-MnO2, from formation, through dehydration, and through phase transformation, with a combination of neutron and X-ray total scattering, extended X-ray absorption fine structure, and neutron vibrational spectroscopy analyses. Models incorporating quantified turbostratic stacking disorder and interlayer/surface chemistry reveal that interlayer water molecules and hydrogen bonding play key roles in maintaining long range stacking coherence, while Mn vacancies within the MnO2 layers promote the intercalation of Cu2+ into interlayer spaces, forming strongly distorted interfacial octahedra. Hydration levels and vacancy concentration are observed to have a marked influence on the charge/discharge capacity and cycling abilities of samples studied. This example informs structure-property optimization strategies for the wider family of layered transition metal oxide-based energy materials, and highlights a broader theme of our research aimed at extracting structure models from experimental data with the detail needed to guide and validate modern nanoscale theories and improve understanding of geologically and technologically significant materials.