The aim of this study is to investigate and develop a phytoremediation method for the removal of two triphenylmethane dyes (crystal violet and malachite green) using an aquatic plant, Lemna minor. The effects of operational parameters such as aquatic plant quantity, initial dye concentration, initial pH of the solutions and temperature of the medium were studied in order to determine the optimum phytoremediation conditions. The plant's photosynthetic pigments were determined quantitatively in order to detect the plant's response to abiotic stress. During the phytoremediation experiments the parallel sub-processes (phytosorption, phytoextraction, phytodegradation) were observed and analysed. The mechanisms of phytoremediation were studied using Fourier transformation infrared spectroscopy, ultraviolet-visible spectroscopy, thin layer chromatography and Energy-dispersive X-ray spectroscopy. Results show that the plant tolerated high concentrations (300 mg/L) of dyes, and was able to remove from the environment and accumulate in its cells the dyes up to a significant percentage (crystal violet was removed by about 80% and malachite green by 90%).