The present study analyzed the levels of Fe, Cu, Mn, Zn, Ni, Pb and Cd in water, sediment and macrophytes (viz Potamogeton crispus and Trapa natans) of Shallabugh wetland from December 2017 to November 2018 at three selected sites. The values of heavy metals in water and sediment reflected higher concentrations in winter at site II and lower in summer at site I. However, macrophytes accumulated high concentrations of heavy metals during summer at site II and lower values during autumn at site I. In water, all heavy metals were found within EPA limits except Fe and Mn and sediments were classified as non-polluted. In macrophytes Cu, Zn and Ni were found below WHO limits, whereas, Pb and Cd were above the limits. The contamination factor for all heavy metals was < 1 except for Cd which show moderate degree of contamination (CF < 3). The pollution load index values were < 1 and geoaccumulation index values were < 0 indicates unpolluted sediment. The bioconcentration factor for both the macrophytes was > 1, hence both the species can be regarded as potential phytoremediators. The correlation analysis indicates a significant positive dependency between water and sediment whereas negative correlation was observed between heavy metals in water and sediment with macrophytes (p < 0.01). The study suggests continuous assessment of water, sediment and macrophytes in order to serve as a useful link for indicating pollution levels and to minimize the potential health hazards.