We report the biodegradation of dye pollutants by a green process that combines the microbial activity of activated sludge with phytoremediation ability of the aquatic plant L. gibba. The obtained results showed that the combination of the two processes when the pollutant was present at concentration of 50 mg/L, lead to a dye removal of 95 and 70% for VB-20 and DR-89, respectively. The biodegradability index based on COD and BOD5 measurement was equal to 3.1 for DR-89 and 2.0 for VB-20, confirming that DR-89 was removed by biosorption phenomena and only VB-20 was transformed into biodegradable compounds. UV-visible, FT-IR and LC/MS analysis were used as a tool for the monitoring of the biodegradation metabolite and the results showed that VB-20 biodegradation occurred by the cleavage of anthraquinone cycle and transformation of aromatic compounds to light hydrocarbon chain; this was further confirmed by the calculation of Fukui index using DFT method. This study highlighted the synergy between the phytoremediation and biodegradation process for organic dye removal.