In this work, we reveal the impact of moisture-induced chemical degradation and proton–lithium exchange on the Li-ion dynamics in the bulk and the grain boundaries and at the interface with lithium metal in highly Li-conducting garnet electrolytes. A direct correlation between chemical changes as measured by depth-resolved secondary ion mass spectrometry and the change in transport properties of the electrolyte is provided. In order to probe the intrinsic effect of the exchange on the lithium kinetics within the garnet structure, isolated from secondary corrosion product contributions, controlled-atmosphere processing was first used to produce proton-free Li6.55Ga0.15La3Zr2O12 (Ga0.15-LLZO), followed by degradation steps in a H2O bath at 100 °C, leading to the removal of LiOH secondary phases at the surface. The proton-exchanged region was analyzed by focused ion beam secondary ion mass spectrometry (FIB-SIMS) and found to extend as far as 1.35 μm into the Ga0.15-LLZO garnet pellet after 30 min in H2O. Impedance analysis in symmetrical cells with Li metal electrodes indicated a greater reactivity in grain boundaries than in grains and a significantly detrimental effect on the Li transfer kinetics in the Li metal/garnet interface correlated to a 3-fold decrease in the Li mobility in the protonated garnet. This result indicates that the deterioration of Li charge transfer and diffusion kinetics in proton-containing garnet electrolytes have fundamental implications for the optimization and integration of these systems in commercial battery devices.