In conclusion, we have deciphered the atomic structures of confined water in layered-phase δ-MnO₂ and the corresponding proton dynamic behavior. The interlayer distance between MnO₂ slabs and the concentration of protons in the interlayer space are demonstrated to be critical factors dictating the local chemical environments of hydrogen bonds. The insights in this work will deepen our understanding of confined proton transport and facilitate the design of proton storage electrodes with high capacity and rate capability in the field of rechargeable aqueous batteries.