Salvinia molesta, an aquatic fern was observed to have a potential of degrading azo dye Rubine GFL up to 97% at a concentration of 100 mg/L within 72 h using 60±2 g of root biomass. Both root as well as stem tissues showed induction in activities of the enzymes such as lignin peroxidase, veratryl alcohol oxidase, laccase, tyrosinase, catalase, DCIP reductase and superoxide dismutase during decolorization of Rubine GFL. FTIR, GC-MS, HPLC and UV–visible spectrophotometric analysis confirmed phytotransformation of the model dye into smaller molecules. Analysis of metabolites revealed breakdown of an azo bond of Rubine GFL by the action of lignin peroxidase and laccase and formation of 2-methyl-4-nitroaniline and N-methylbenzene-1, 4-diamine. Anatomical tracing of dye in the stem of S. molesta confirmed the presence of dye in tissues and subsequent removal after 48 h of treatment. The concentration of chlorophyll pigments like chlorophyll a, chlorophyll b and carotenoid was observed during the treatment. Toxicity analysis on seeds of Triticum aestivum and Phaseolus mungo revealed the decreased toxicity of dye metabolites. In situ treatment of a real textile effluent was further monitored in a constructed lagoon of the dimensions of 7 m×5 m×2 m (total surface area 35 m2) using S. molesta for 192 h. This large scale treatment was found to significantly reduce the values of COD, BOD5 and ADMI by 76%, 82% and 81% considering initial values 1185, 1440 mg/L and 950 units, respectively.