Aquatic environments are often contaminated with various compounds, with potential toxicity towards aquatic organisms, which may enter the food chain. Azo dyes are used in various industries and contamination of waters has been reported. The present paper assesses the toxicity of the synthetic, water soluble Congo Red dye towards Lemna minor from a physiological and cytogenetical point of view. The dye was tested in 5-5000 ppm concentrations. Total frond surface, root growth and fresh mass reductions were registered from 5 ppm dye concentration, with a concentration-dependent response and calculated EC50 of 1530 ppm. Plant growth was completely inhibited above 2500 ppm. Dye accumulation was observed in tissues, along with necrosis formation. Chlorophyll a contents decreased, while carotenoid contents increased above 2500 ppm. Significant inhibition of PSII efficiency was recorded above 1000 ppm. Mitotic indices were decreased at 5 and 1000 ppm dye and were 0 at 5000 ppm. The number of chromosomal aberrations significantly increased at 5 and 1000 ppm dye. The growth medium was decontaminated up to 56% at 250 ppm dye concentration by Lemna plants. Congo Red azo dye presented toxicity towards Lemna minor, from a physiological and cyotgenetical point of view, especially at higher concentrations. In the same time, a phytoremediation potential of duckweed with respect to the tested dye was demonstrated.