Developed areas of the coal industry are subjected to long-term anthropogenic impacts from the input and accumulation of overburdened coal material, containing potentially toxic heavy metals and metalloids (HMM). For the first time, comprehensive studies of soils and plants in the territory of the Donetsk coal basin were carried out using X-ray fluorescence, atomic absorption analysis, and electron microscopy. The observed changes in the soil redox conditions were characterized by a high sulfur content, and formations of new microphases of S-containing compounds: FeS2, PbFe6(SO4)4(OH)12, ZnSO4·nH2O, revealed the presence of technogenic salinization, increased Сorg content, and low pH contents. Exceedances of soil maximum permissible concentrations of Pb, Zn, Cu, and As in areas affected by coal dumps were apparent. As a consequence of long-term transformation of the environment with changes in properties and chemical pollution, a phytotoxic effect was revealed in Phragmites australis (Cav.) Trin. ex Steud, accompanied by changes in ultrastructural and organization features of roots and leaves such as increases in root diameters and thickness of leaf blades. The changes in the ultrastructure of cell organelles: a violation of the grana formation process, an increase in the number of plastoglobules, a decrease in the number of mitochondrial cristae, and a reduction in the electron density of the matrix in peroxisomes were also observed. The accumulation of large electron-dense inclusions and membrane fragments in cell vacuoles was observed. Such ultrastructural changes may indicate the existence of a P. australis ecotype due to its long-term adaptation to the disturbed environment.