Crystallization water plays an important role in the self-organization of oligomer chains in conducting polyaniline. In order to quantify the interaction between emeraldine salt and such a water, models containing a tetramer in bipolaronic or polaronic form, chloride counterions, and an explicit water molecule are used. Different initial positions of water with respect to the oligomer chain-tangential and vertical-are considered. Various media are simulated by introducing an implicit solvent continuum of decreasing polarity. The DFT-D3/PCM computational approach is employed to examine the behavior of the systems in several aspects-the role of the explicit water position and the effect of the environment polarity on the spatial structure, energetics, charge distribution, and the frontier molecular orbital energies. The strength of hydrogen bonding and the patterns of charge redistribution invoked by the water molecule are discussed. The study establishes trend lines in the variation of the molecular characteristics upon change of milieu as a tool for control of the self-assembly process. The results show that chains interact more efficiently with tangentially placed water. The influence of the environment polarity is minor and is mainly expressed in slight shortening of the intermolecular distances and mild decrease of the group charges of the system components with reduction of polarity.