Structure of soil organic matter (SOM) is a hot topic of discussion among scientific community for several decades. The mostly discussed models, among many, are polymer model and supramolecular model. While the former considers SOM as macromolecules consisting of amorphous and crystalline domains, the latter explains SOM as a physicochemical entity dominated by weak hydrophobic and H-bond interactions in the secondary level, which holds individual molecules of primary structure together. The weak forces in secondary level impart characteristic mobility of SOM. Very important consequence of this multidimensional formulation is that physicochemical structure plays a crucial role in most biogeochemical functions of SOM, apart from the chemical composition. Recently introduced concept of cation and water molecule mediated bridges between OM molecular segments (CaB and WaMB, respectively) evolved from physicochemical understanding of SOM structure. Even though several indirect evidences were produced for CaB and WaMB during last years, no clear-cut understanding of these processes has been achieved yet. Experimental difficulty due to overlapping effects of equally important CaB-governing parameters such a pH and competing cations raises huge challenge in investigating CaB-related influences. This thesis, therefore, aims to validate an experimental set-up for inducing CaB within OM structures and assessing it from various chemical and physicochemical aspects. The method involved removal of omnipresent cations and adjustment of pH before cation addition. This helped to separate pH effects and cation effects. Based on results obtained on two different types of organic matter, it can be deduced that multivalent cations can cross-link SOM, given that functional group density of the SOM material is enough for the functional groups to be arranged in sufficient spatial proximity to each other. Physicochemical structural reorganisation during aging causes formation of more and/or stronger CaB and WaMB. As for inducing CaB directly after cation treatment, cationic size and valency were found determinant also for aging effect. A strongly cross-linked system in the beginning is less vulnerable to structural changes and undergoes aging with lower intensity, than an initially weakly cross-linked system. Responsible for the structural changes is, the inherent mobility of SOM within its physicochemical assemblage. Thus the information on structural requirement of CaB and its consequences on OM matrix rigidity will help to obtain insight into the physicochemical SOM structure. Additionally, organic matter quality (assessed by thermal analysis) and pore structure of SOM formed in a set of artificial soils showed that mineral materials are important for the chemical nature of SOM molecules, but not for the physical structure of organo-mineral associations, at least after several months of SOM development. Furthermore, nanothermal analysis using atomic force microscopy (AFM-nTA) was implemented in soils for the first time to reveal nanoscale thermal properties and their spatial distribution in nano- and micrometer scales. This helped to identify physicochemical processes, such as disruption of WaMB, in low-organic soils, in which bulk methods fail due to their low sensitivity. Further, various types of materials constituting in soils were distinguished with high resolution by advanced application of the method, in combination with other AFM parameters. Attempts were done to identify various materials, with the usage of defined test materials. Above all, the method is potent to reveal microspatial heterogeneity on sample surfaces, which could help understanding process-relevant hotspots, for example. This thesis thus contributes to the scientific understanding on physicochemical structural dynamics via cross-linking by cations and via nanoscale thermal properties. Direct investigation on CaB demonstrated here will potentially help making a big leap in knowledge about the interaction. The observed aging effects add well to the understanding of supramolecular consideration of SOM. By introducing nanothermal analysis to the field of soil science, it is made possible to face the problem of heterogeneity and spatial distribution of thermal characteristics. Another important achievement of AFM-nTA is that it can be used to detect physicochemical processes, which are of low intensity.