Soil organic matter (SOM) is a key component responsible for sequestration of organic molecules in soil and regulation of their mobility in the environment. The basic structure of SOM is a supramolecular assembly responding dynamically to the environmental factors and the presence of interacting molecules. Despite of the advances in the understanding of sorption processes, the relation between sorbate molecules, SOM supramolecular structure and its dynamics is limited. An example of a dynamic nature of SOM is a physicochemical matrix aging that is responsible for SOM structural arrangement. The underlying process of the physicochemical aging is the formation of water molecule bridges (WaMB) between functional groups of molecular segments. Since WaMB influence the stiffness of SOM structure, it was hypothesized that formation of WaMB contributes to the sequestration of organic molecules. However, this hypothesis has not been tested experimentally until now. Furthermore, the knowledge about the influence of organic molecules on WAMB is based solely on computer modeling studies. In addition, the influence of organic molecules on some physical phases forming SOM is not well understood. Especially, the interactions between organic molecules and crystalline phases represented by aliphatic crystallites, are only presumed. Thus, the investigation of those interactions in unfractioned SOM is of high importance. In order to evaluate the involvement of WaMB in the sequestration of organic molecules and to increase our understanding about interactions of organic chemicals with WaMB or aliphatic crystallites, the following hypotheses were tested experimentally. 1) Similarly to crystalline phases in synthetic polymers, aliphatic crystallites, as a part of SOM, cannot be penetrated by organic molecules. 2) The stability of WaMB is determined by the ability of surrounding molecules to interact with water forming WaMB. 3) WaMB prevent organic molecules to leave the SOM matrix and contribute thus to their immobilization. In order to test the hypotheses 1 and 2, a set of experiments including treatment of soils with chosen chemicals was prepared. Interaction abilities of these chemicals were characterized using interaction parameters from the Linear Solvation Energy Relationship theory. WaMB characteristics were monitored using Differential Scanning Calorimetry (DSC) allowing to measure the WaMB thermal stability and the rigidity of SOM matrix; which in turn was determined by the heat capacity change. In addition, DSC and 13C NMR spectroscopy assessed thermal properties and the structure of aliphatic crystallites. The spiking of samples with a model compound, phenol, and measurements of its desorption allowed to link parameters of the desorption kinetics with WaMB characteristics. The investigation showed that the WaMB stability is significantly reduced by the presence of molecules with H-donor/acceptor interaction abilities. The matrix rigidity associated with WaMB was mainly influenced by the McGowan’s volume of surrounding molecules, suggesting the importance of dispersion forces. The desorption kinetics of phenol followed a first order model with two time constants. Both of them showed a relation with WaMB stability, which supports the hypothesis that WaMB contribute to the physical immobilization of organic molecules. The experiments targeted to the crystallites revealed their structural change from the ordered to the disordered state, when in contact with organic chemicals. This manifested in their melting point depression and the decrease of overall crystallinity. Described structural changes were caused by molecules interacting with specific as well as non-specific forces, which suggests that aliphatic crystallites can be penetrated and modified by molecules with a broad range of interaction abilities. This work shows that chosen organic molecules interact with constituents of SOM as exemplified on WaMB and aliphatic crystallites, and cause measurable changes of their structure and properties. These findings show that the relevance of aliphatic crystallites for sorption in soil may have been underestimated. The results support the hypothesis that physicochemical matrix aging significantly contributes to the immobilization of organic chemicals in SOM.