Using the mutually consistent variant of the integral equation polymer reference interaction site model (RISM) theory and the chemically realistic rotational isomeric state (RIS) model, we perform a molecular level modeling of the specific structural organization of perfluorosulfonic acid ionomer (Nafion) with certain amount of physisorbed water. Our results establish molecular scale information necessary for understanding the equilibrium structure and thermodynamics of water‐containing Nafion as well as water distribution and ionic (molecular) transport phenomena in hydrated Nafion membranes. As a first step in this direction, semi‐empirical quantum mechanical calculations on the molecular structures and energies of the polymeric backbone and pendant chains of Nafion with and without additional water molecules are carried out. These data are used in the single‐polymer RIS Monte Carlo simulation, in which the short‐range intramolecular interactions are taken into account via appropriate matrices of statistical weights. The local structure and morphology of the entire bicomponent water‐containing system is calculated consistently on the basis of the RISM theory at different contents of absorbed water. We find that the addition of even a relatively small amount of water leads to the strong intensification of aggregation processes observed for polar sulfonic acid (SO3H) groups. Water molecules and polar SO3H groups form mixed aggregates with a three‐layer structure. Incorporation of water molecules inside the aggregates results in an increase of their stability and leads to the increase of the number of associating groups in a stable aggregate. With increasing the number of incorporated solvent molecules, the average size of mixed aggregates increases. The results obtained in the present study support the concept of an irregularly shaped cluster surfaces. Such geometries are favorable to the formation of long channels of connected water‐containing aggregates providing the unique permeability characteristics of Nafion membranes. In addition, we investigate the clustering and continuum percolation in the water phase, using the formalism of pair‐connectedness correlation functions. The mean cluster size found theoretically is in reasonable agreement with the corresponding experimental estimates existing in the literature.

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