The effect of eutrophication, water exchange and suspended solids on the state of the freshwater bodies used for rearing rainbow trout in cages is analyzed in detail on the basis of the relevant literature and the authors’ own data. The critical total phosphorus concentration in the waters used for trout farming, which should be taken into account when calculating the output of trout farms, is proposed. It is noted that the input of nutrients (phosphorus and nitrogen) from bottom sediments to the water contributes negatively to the eutrophication of water bodies. The deleterious effect of suspended matter on water bodies (zoobenthos and zooplankton) has been revealed. It should be taken into consideration in ecological assessment of water bodies. We show that water exchange in a water body or its individual areas is essential for the siting of trout farms, depending on the location of tributaries and run-off. To prevent irreversible consequences in aquatic ecosystems used for commercial trout farming, hydrological, hydrochemical and hydrobiological indices should be monitored.