Organic pollutants, such as dyes, have a negative effect on the aqueous environment, therefore, their elimination from water bodies is a high priority. In this work, Eichhornia crassipes and Salvinia natans, both model plants with high phytoremediation efficiency, were exposed to various concentrations (Ci = 50–500 mg/L) of Eriochrome Black T (EBT). Their capacity to assimilate EBT was studied for 16 days of exposure, similar to natural conditions and by spectrophotometric monitoring of the dye concentration (EE. crassipes; 150 mg/L = 33%; ES. natans; 150 mg/L = 71.5%). The changes of the experimental parameters (pH—equalised by day 5, temperature, humidity, light intensity) were followed, and plant growth and biochemical responses to toxic stress effects (photosynthetic pigments, Energy-dispersive X-ray spectroscopy (EDX)—decreased effect of P, Mg, Ca, S and K, Scanning electron microscopy (SEM), defense enzyme) were examined. Furthermore, changes in oxidative- and photo-degradation of EBT in time and the solid-state properties (SEM, EDX, Fourier-transform infrared spectroscopy-FTIR) of the dye were investigated. Our results demonstrate that, despite the toxic stress, both species succeeded in reducing the dye-concentration of the water and S. natans proved to be more efficient in binding and removing organic dyes. With our findings, we proved that both plants alleviated the abiotic stress of dye contamination.