The stabilizing effect of water molecule bridges on polar regions in humic substances (HSs) has been investigated by means of molecular dynamics (MD) simulations. The purpose of these investigations was to show the effect of water molecular bridges (WAMB) for cross-linking distant locations of hydrophilic groups. For this purpose, a tetramer of undecanoid fatty acids connected to a network of water molecules has been constructed, which serve as a model for spatially fixed aliphatic chains in HSs terminated by a polar (carboxyl) group. The effect of environmental polarity has been investigated by using solvents of low and medium polarity in force-field MD. A nonpolar environment simulated by n-hexane was chosen to mimic the stability of WAMB in a hydrophilic hotspot surrounded by a nonpolar environment, while the more polar acetonitrile environment was chosen to simulate a more even distribution of polarity around the carboxylic groups and the water molecules. The dynamics simulations show that the rigidity of the oligomer chains is significantly enhanced as soon as the water cluster is large enough to comprise all four carboxyl groups. Increasing the temperature leads to evaporization processes which destabilize the rigidity of the tetramer-water cluster. Embedding it into the nonpolar environment introduces a pronounced cage effect which significantly impedes removal of water molecules from the cluster region. On the other hand, a polar environment facilitates their diffusion from the polar region. One important consequence of these simulations is that although the local water network is the stabilizing factor for the organic matter matrix, the degree of stabilization is additionally affected by the presence of nonpolar surroundings.