Water molecules in soil organic matter (SOM) can form clusters bridging neighboring molecular segments (water molecule bridges, WaMBs). WaMBs are hypothesized to enhance the physical entrapment of organic chemicals and to control the rigidity of the SOM supramolecular structure. However, the understanding of WaMBs dynamics in SOM is still limited. We investigated the relation between WaMBs stability and the physicochemical properties of their environment by treating a sapric histosol with various solvents and organic chemicals. On the basis of predictions from molecular modeling, we hypothesized that the stability of WaMBs, measured by differential scanning calorimetry, increases with the decreasing ability of a chemical to interact with water molecules of the WaMBs. The interaction ability between WaMBs and the chemicals was characterized by linear solvation energy relationships. The WaMBs stability in solvent-treated samples was found to decrease with increasing ability of a solvent to undergo H-donor/acceptor interactions. Spiking with an organic chemical stabilized (naphthalene) or destabilized (phenol) the WaMBs. The WaMBs stability and matrix rigidity were generally reduced strongly and quickly when hydrophilic chemicals entered the soil. The physicochemical aging following this destabilization is slow but leads to successive WaMBs stabilization and matrix stiffening.