Hydrated materials contain crystal water within their crystal frameworks and can exhibit extraordinary properties as a result. However, a detailed understanding of the mechanism involved in the hydration process is largely lacking, because the overall synthesis process is very difficult to monitor. Here, we elucidate how the insertion of crystal water mediates an anomalous spinel-to-Birnessite phase transition during electrochemical cycling in aqueous media. We find that, at the initial stage of the phase transition, crystal water is inserted into the interlayer space between MnO6 layers in the form of a hydronium ion (H3O+). The H3O+ insertion is chemically driven in the reverse (reducing) direction to the applied anodic (oxidizing) electric field, stabilizing the structure and recovering the charge balance following the deinsertion of Mn2+. A comparative investigation using various electrolyte solutions revealed that the H3O+ insertion competes with the insertion of other ionic charge carriers (Li+, Na+, and Mg2+), and the overall efficiency of the phase transition is determined by this competition. This understanding of crystal water insertion offers an insight into strategies to synthesize hydrated materials.