The present investigation deals with the aquatic macrophyte diversity and species composition along the lower reaches of the second longest river of Kerala, the Bharathapuzha River, also known as Nila. 110 plants of aquatic and shore vegetation belonging to three Pteridophyta and 38 Angiosperm families were enumerated. 23% of the vegetation analysed were grasses and sedges and 34% of plants were of medicinal importance. Aquatic and wetland plant communities are bioindicators of environmental quality. In the present study 25% of the plants recorded were exotic and invasive weeds indicating that the river ecosystem is being transgressed.