The study detailed in this paper is about the determination of the physical–chemical parameters of water, after keeping it in prolonged contact with the Nafion polymer. The parameters under study are: electrical conductivity, χ (μS cm−1); heat of mixing with acid (HCl), ΔQmixHCl (J kg−1) or basic (NaOH) solutions, ΔQmixNaOH (J kg−1), and pH. χ increases of up to two orders of magnitude, ΔQmixNaOH (J kg−1) is exothermic and increases as the electrical conductivity increases, with a roughly linear trend, up to one order of magnitude. The analogous ΔQmixHCl (J kg−1), on the contrary, is found to be null. The pH is quite acid and shows a very good linear correlation with log χ. The linear correlations hint at a single cause for the variation of the three very different physical–chemical parameters. This complex and hard to rationalize phenomenology, finds a good theoretical support in the work hypothesis of the formation of dissipative structures within the liquid. These are far-from-equilibrium systems outside the paradigm of classical thermodynamics. The work hypothesis of the formation of molecular aggregates of water molecules (dissipative structures, aqueous nanostructures, clusters, coherence domains, etc.) is shared with two other aqueous systems obtained with different preparation protocols, so we briefly recall them here: (1) EDS (extremely diluted solutions): obtained through an iterative process of successive dilutions and agitations. (2) IFW (iteratively filtered water): obtained through an iterative process of successive filtrations through sintered glass filters. (3) INW (iteratively nafionized water): obtained through an iterative process of successive drying and wetting of the Nafion polymer. Each protocol produces water exhibiting its own peculiarities, to the point that they can be considered different, albeit with the common element of a variation of the super-molecular structure of the water solvent. The physical–chemical properties of these perturbed waters cannot be framed by the paradigm of classical thermodynamics, but rather require the use of the thermodynamics of systems far from the equilibrium and of irreversible processes.