To simulate the processes that take place at the polypyrrole/water interface under different states of oxidation of the polymer, a reliable model of the polymer/water system is necessary. To this end, a model with atomic detail of the polypyrrole/water system was simulated for first time in both the oxidized (charged) and reduced (uncharged) polymer. The system consists of a single layer of water molecules between two layers of polypyrrole film. Each polymer film was formed of 64 polymeric chains of 10 monomeric units each, and after oxidation of each polypyrrole chain, 128 chloride ions were included to maintain the electroneutrality of the system. In this way, a classical molecular dynamics simulation was carried out for both oxidized and reduced polypyrrole. From the simulated trajectories, macroscopic properties, such as the polypyrrole density in its reduced state and polymer swelling after oxidation, were simulated. Thus, valuable information related to the atom distribution profile and water and counterion permeation across the polymer/water interface was obtained. In this regard, due to the high hydrophobicity of the reduced polypyrrole, water molecules were repelled from the core of the polymer matrix and so did not penetrate into the polymer matrix, at least during our simulations. As a consequence of this hydrophobicity, a sharp polymer/water profile was obtained. In the case of the oxidized polypyrrole, chloride ions penetrated into the core of the polymer matrix to keep the electroneutrality of the system. As a result of this ion penetration into the polymer and the strong polymer polymer repulsions between charged sites inside the oxidized polypyrrole, a swelling of the polymer matrix of 11% was measured, while the thickness of the polypyrrole/water interface increased by 50% compared with its reduced state. Finally, charge distribution and electric potential profiles across the polypyrrole/water interface were obtained in both oxidized and reduced states. The contribution of water to the electric potential which consists of reorientating its dipoles was measured in both states.