The present study aimed to investigate the surface water quality and heavy metal accumulation potential of Salvinia natans [(L.) All.] in three prominent lakes: Dal, Manasbal, and Wular, in Jammu and Kashmir, North India. Water and plant sampling was conducted from August to October 2024 and analyzed for physicochemical and eight heavy metal (Cd, Cr, Cu, Ni, Pb, Fe, Mn, and Zn) parameters following standard methods. Water quality among the selected lake systems showed significant variation, while the majority of parameters exceeded the surface water quality standards. The concentration of heavy metals was found to be higher in the root tissues of S. natans than in the leaves across all lakes, with Dal Lake showing the highest accumulation. Furthermore, the bioconcentration and translocation factors (BCF and TF) revealed that S. natans could function as hyperaccumulator plants, as indicated by values greater than 1. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) revealed distinct pollution profiles for Dal, Manasbal, and Wular lakes, with Dal Lake being the most polluted. In addition, the multiple linear regression modeling also established predictive relationships between water quality parameters and heavy metal uptake by S. natans plant tissue. The present study showed that selected lake systems of North India are being impacted by ongoing anthropogenic activities and require effective pollution mitigation strategies and regular monitoring to preserve the lakes’ ecological health and water quality. The presence of S. natans has been demonstrated to contribute to the restoration of lacustrine ecosystems through the uptake of heavy metals from the water.