Thamirabarani river acquires large untreated sewage effluents from the Tirunelveli and Thoothukudi districts of South Tamil Nadu. This study examined the concentration of trace elements in water, sediment, and phytoaccumulation potential of aquatic weeds viz., A. cristata, E. crassipes, S. natans, and P. stratiotes, growing along Srivaikundam dam of Thamirabarani river. The Pb, As, Hg, Cd, and Ni concentrations in water were slightly higher than the US Food and Drug Administration (USFDA) drinking water guidelines; however, their accumulation in sediment was below WHO's sediment quality guideline. This study concludes that the phytoaccumulation factor (PAF) and translocation factor (TF) was >1 in E. crassipes and A. cristata, representing them as hyperaccumulators, suitable for phytoremediation in polluted localities. E. crassipes, A. cristata, and S. natans accumulated (100–500 fold) higher trace elements concentrations than that present in the water. Also, the concentrations of trace elements found in the aquatic weeds were below the recommended levels for the critical plant range (CRP). These selected aquatic weeds are more suitable for plant hybridization to be modified as superbug plants.