Geochemical barriers are the special type of natural systems boundaries. They prevent the penetration of some of substances and are open for the migration of others. For the inorganic substances, especially for the metal ions the barriers are studied enough completely: the models of barriers are developed, the penetration and accumulation kinetic is assessed. But for the organic compounds the role of the geochemical barriers is practically not studied. Especially important are such assessments from the point of view of migration and accumulation analyses of supertoxic compounds. Assessed the role of polycyclic aromatic compounds (PAHs) as most sensitive markers of the geochemical barriers. For the first time for organic substances of this group, estimated the rate of penetration through geochemical barriers and accumulations in media. The relative chemical stability of PAHs and their toxicity make them a priority object for the geochemical studies. In the presented study analyzed the ability of PAHs to migration through different kinds of boundaries in the aquatic systems: boundaries-divisions and boundaries-barriers at the contact of ices, water, snow, bottom sediments; boundaries in the system with an active technogenic pressure in the Aojan river catchment area (China, leather industry region); boundaries in the “background” region (PAHs migration in the system “soil – plants”, “water – bottom sediments”). Analyzed the conditions of accumulation, of the PAHs penetration activity through the geochemical boundaries. The use of the modern multivariate methods allows us to identify the identity of the migration and accumulation processes in different environments and different geographic conditions. PAHs are an effective marker of geochemical boundaries. All of the PAH compounds are more or less subject to transformation, the maximum of which is achieved on the boundaries-divisions. Even within relatively homogeneous phases due to phase transitions, an active selectively transformation of the PAHs ensemble takes place. Phase transitions, both in heterogeneous media and at the boundaries-divisions occur more intensively than in homogeneous media. The involvement of organic substances (even at the level of phenomenological models) radically changes the understanding of the interrelations between the components in the geochemical system. Extremely active (change of concentrations tens to thousands of times) the accumulation of PAHs occurs in a system involving living matter. Its introduction into the general scheme of the aquatic systems elements (even at the phenomenological level) changes fundamentally our ideas about the functional significance of the biota in the structure of the matter flows in the aquatic ecosystems. © SGEM2017.