Transition metal oxides are often the materials of choice for energy storage and conversion applications due to their numerous oxidation states, mixed electronic/ionic conductivity, and structural variability. Here, we describe the electrochemical behavior of hydrous hexavalent tungsten and molybdenum oxides (WO₃ and MoO₃, respectively) as model material systems for investigating aqueous intercalation mechanisms.  These oxides offer the benefits of multi-valent transition metal redox, diversity of crystal structure, hydrated polymorphs, and a variety of synthesis techniques that yield bulk powders, nanomaterials, and nanosheets.  The mechanism of ion intercalation is dependent upon two different regions of the material:  the internal structure, or the solid-state environment that controls the ion diffusion and favorable storage sites, and the external surface, or the nature of the electrochemical interface which controls the charge-transfer step of the intercalation reaction as well as stability.  We characterize the behavior of these oxides in a variety of aqueous electrolytes in order to understand the effect of electrolyte ion size, charge, and hydration on the intercalation mechanism. We find that the presence of structural water and the nature of the intercalating ion both result in significant effects on the aqueous intercalation mechanism in tungsten and molybdenum oxides.