The current study provides an information on the combined effect of pollution with potentially toxic elements (PTEs) and polycyclic aromatic hydrocarbons (PAHs) in hydromorphic soils on the accumulation, growth, functional and morphological-anatomical changes of macrophyte plant, i.e., Phragmites australis Cav., as well as information about their bioindication status on the example of small rivers of the Azov basin. The territory of the lower reaches of the Kagalnik River is one of the small rivers of the Eastern Azov region was examined with different levels of PTEs contamination in soils, where the excess of the lithosphere clarkes and maximum permissible concentrations (MPC) for Mn, Cr, Zn, Pb, Cu, and Cd were found. The features of the 16 priority PAHs quantitative and qualitative composition in hydromorphic soils and P. australis were revealed. The influence of soil pollution on accumulation in P. australis, as well as changes in the morphological parameters were shown. It has been observed that morphometric changes in P. australis at sites experiencing the сontamination and salinity are reflected with the changes in the ultrastructure of plastids, mitochondria, and EPR elements of plant cells. PTEs accumulated in inactive organs and damaged cell structures. At the same time, PAHs penetrated through the biomembranes and violated their integrity, increased permeability, resulted cell disorganization, meristem, and conductive tissues of roots. The nature and extent of the structural alterations found are dependent on the type and extent of pollution in the examined regions and can be utilized as bioindicators for evaluating the degree of soil phytotoxicity characterized by the accumulation of PTE and PAHs.