Water–ions interactions and spatial confinement largely determine the properties of hydrogen-bonded nanomaterials. Hydrated acidic polymers possess outstanding proton-conducting properties due to the interconnected H-bond network that forms inside hydrophilic channels upon water loading. We report here the first far-infrared (FIR) coupled to mid-infrared (MIR) kinetics study of the hydration mechanism in benchmark perfluorinated sulfonic acid (PFSA) membranes, e.g., Nafion. The hydration process was followed in situ, starting from a well-prepared dry state, within unprecedented continuous control of the relative humidity. A step-by-step mechanism involving two hydration thresholds, at respectively λ = 1 and λ = 3 water molecules per ionic group, is assessed. The molecular environment of water molecules, protonic species, and polar groups are thoroughly described along the various states of the polymer membrane, i.e., dry (λ ≈ 0), fully ionized (λ = 1), interacting (λ = 1–3), and H-bonded (λ > 3). This unique extended set of IR data provides a comprehensive picture of the complex chemical transformations upon loading water into proton-conducting membranes, giving insights into the state of confined water in charged nanochannels and its role in driving key functional properties as ionic conduction.