The reduction of tetravalent manganese (Mn(IV)) to trivalent manganese (Mn(III)) by HEPES Good’s buffer is often used to modify the reactivity of δ-MnO2 and to distinguish between the Mn(III) and Mn(IV) oxidants in redox reactions. However, the structure of HEPES-reacted δ-MnO2 has remained elusive, hindering a detailed understanding of interfacial electron transfer between adsorbed species and structural Mn. Here, we characterized the structure of δ-MnO2 reacted with HEPES at pH 6 and 8 under low and high NaCl ionic strength, using chemical analysis, high-energy X-ray diffraction, pair distribution function (PDF), extended X-ray absorption fine structure (EXAFS) spectroscopy, and high-resolution transmission electron microscopy (HRTEM) coupled with selected area electron diffraction (SAED). The average Mn oxidation state (AMOS) decreases from 3.92−3.87 to 3.71–3.59 after HEPES addition, depending on pH and ionic strength. HEPES-reacted δ-MnO2 has a distinctly different structure at low and high ionic strength. At low ionic strength, the δ-MnO2HE crystallites are 3–6 nm across, and the MnO2 layers have approximately 23% vacant sites capped with mainly Mn(III) and some Mn(II). At high ionic strength and pH 8, δ-MnO2HE contains large crystals, several hundred nanometers across, made up of crystallographically oriented nanodomains. Most SAED patterns show streaks along the [100]* direction, indicating a high degree of disorder in the close packing of the anionic sheets, in the Na position within the interlayer, and in the Mn(IV)–Mn(III) distribution within the layer. Some nanodiffraction patterns show distinct superstructure reflections along the streaks with A* = 3a*, as seen in well-crystallized triclinic birnessite, and A* = 6a*. High-ionic-strength δ-MnO2HE has no interlayer Mn(III), and the Na(I) ions, along with the layer Mn(III) and Mn(IV) cations, are semiordered at the short- to medium-range scales and essentially disordered over longer distances. Identifying the two distinct structures of HEPES-reacted δ-MnO2 clarifies structural ambiguities reported in the literature and provides a solid foundation for exploring its redox reactivity and electrochemical performance.