This work investigates the physicochemical alterations of water perturbed by prolonged contact with the hydrophilic polymer Nafion, referred to as iteratively nafionized water (INW). The parameters measured are: electrical conductivity, χ  μS cm −1 , heat of mixing with basic sodium hydroxide (NaOH) solutions, Δ Q NaOH mix  J kg −1 , and pH. The results indicate that supramolecular aggregates of water molecules form after prolonged contact with a Nafion surface. Analytical determination by ion chromatography allows us to exclude the role of contaminants. This suggests that water may possess an exceptional self-organization capability triggered by the contact with a hydrophilic surface. Conductometric, pH-metric, and calorimetric titrations of INW were performed by the addition of NaOH solutions to determine the concentration of the aqueous nanostructures, via conductometric and pH-metric titration with NaOH solutions. Thermodynamic parameters were determined via calorimetric titration, for the process of formation of complexes between the nanostructures and the base used.