Fungi play an important role in the degradation of dead leaves and other plant detritus in aquatic environments. Aquatic fungi secrete enzymes that degrade polysaccharides and other polymers. Fungi are also efficient in the biodegradation of recalcitrant compounds like xenobiotics, lignin and dye stuffs by their extra cellular ligninolytic enzyme system. Hence, the present study was aimed at using aquatic fungi in the bioremediation of waste water. The selected species were Aspergillus niger, Rhizopus arrhizus, Penicillium citrinum and Fusarium oxysporum which were isolated from the River Cauvery collected from Upper Anicut (Mukkombu). Results indicate that all the four fungal species helped in decreasing the levels of BOD, COD and nutrients like PO4 and nitrate. However, each species responded differently. Nevertheless, among the four fungal species studied, Aspergillus niger showed the most promising results and it appears to be the best candidate for bioremediation.