Small rivers are the most sensitive objects in the hydrographic network, which are still understudied hydrologically and hydrobiologically. These are upper links in major landscape systems primarily reflecting adverse consequences of economic activities. The heavy metal pollution affects the whole “water-sediments-plants” system and leads to cumulative consequences, thereby posing health risks to the public in the affected region. As part of this research, hydrobiological indicators of aquatic landscape systems at the Filippovka riv. were studied, the major polluting components in environmental compartments identified and the extent of pollution and exceeded maximum permissible concentration (MPC) of heavy metals in bottom sediments defined. In order to research into the anthropogenic biotope pollution by products of the mining plant’s discharges in the region, indices of periphytic saprobity were identified, water quality class from developmental factors of phytoplankton and macrozoobenthos was defined, the toxic effect on living organisms and their biodiversity was studied. Dominating species of hydrobionts were identified along with hydrophytes that are able to act as indicators of the transfer of heavy metals from bottom sediments to plants. The index of biological accumulation was estimated, the content of heavy metals in hydrophytes was compared with ground vegetation. Research findings allow the assessment of the bioindication efficiency of industrially polluted waters and the accumulative effect of the transfer of heavy metals in the “water-bottom sediment-plant system”.