The results of the analysis of thermodynamic characteristics of the processes of hydrocarbon amassment in the components of geochemical systems are presented (waters, soils, plants and other substances forming ecosystem). The need to use an ideology and apparatus for calculating thermodynamics is due to the complexity and diversity of mass transfer in interacting media. The material and energy flows of marker compounds, polycyclic aromatic hydrocarbons (PAHs), are analyzed: Naphthalene (Naph), Acenaphthene (Ace), Fluorene (Flourene), Phenanthrene (Phen), Anthracene (An), Fluoranthene (Flu), Pyrene (Py), benzo[a]anthracene (BaA), Chrysene (Chr), Benzo[b]fluoranthene (BbFlu), Benzo[k]fluoranthene (BkFlu), Benzo[a]pyrene (BaP), Benzo[ghi]perylene (Bghi), Dibenzo[a, h]anthracene (DbA), Indeno[1, 2-cd]pyrene (Ip). Estimates are obtained of the intensity of PAH concentration processes in geochemical systems in different states from the point of view of stability, from clearly unstable to metastable. The role of living matter in the formation of stability of geochemical systems is revealed.