The paper investigates the properties of geochemical systems components (GCS) within the thermodynamic framework. In a departure from previous approaches, the maximum possible number of interconnected media in holistic GCS is analyzed using hierarchical classification procedures. The studied sample covers the maximum possible selection of media, which are interconnected in natural systems in real conditions. The paper reports that complex organic compounds, such as polycyclic aromatic hydrocarbons (PAHs) are highly informative indicators of the properties of substances migration in media. Being geochemical markers, these compounds demonstrate the ability to accumulate on geochemical barriers and selectively move in interacting media, which makes them key objects of study. In addition, the marker role of these compounds draws on their “confinement” to several geochemical processes (natural or industrial) and ability to ultimately identify the source of the pollution. The existing accounts fail to describe these mechanisms of mass transfer. The proposed phenomenological models of migration, transformation, and accumulation of PAHs are based on quantitative estimates, which provide more consistent results compared with the descriptive representations of the behavior of substances. This allowed us to identify the role of studied physicochemical characteristics of PAHs in their accumulation in the environmental media. The paper demonstrates that the most active evolution of GCS occurs in case plant media and, in general, living matter is included in their composition. © 2020 Elsevier Ltd