Wetlands are dynamic ecosystems that provide feeding and nesting grounds for diverse species of waterbirds. The quality of wetland habitat may have an impact on the density, diversity, and species richness of waterbirds. Toxic metal contamination is one of the most significant threats to wetland habitats. Feathers are a key indicator of heavy metal contamination in avian communities as a non-invasive method. We examined the levels of Arsenic (As), Cadmium (Cd), Cobalt (Co), Chromium (Cr), Copper (Cu), Lead (Pb), Nickel (Ni), and Zinc (Zn) using ICP-AAS and standards of digestion procedure from the primary feathers of 10 distinct species of waterbirds. The study was conducted at four wetlands, viz., Point Calimere Wildlife Sanctuary (Ramsar site); Pallikaranai Marshland (Ramsar site); Perunthottam freshwater lake (unprotected wetland), Tamil Nadu and the Pulicat Lake, Andhra Pradesh, (Ramsar site), India. The Large crested tern had higher concentrations of As, Co, Cr, and Ni. Cu was greater in the Indian pond heron, and Zn was higher in the Grey heron. The accumulation of metals differed among the waterbirds (p < 0.05), and the inter-correlation of metals found positive influences between the tested metals, i.e., Co was positively associated with As, Cr had a positive correlation with As and Co, and Ni was positively correlated with As, Co, Cr, and Cu. In contrast, Pb had a positive association with Cu and Ni. The Zn was associated with Co, Cr and Cu. The level of metals in waterbirds was Zn > Cu > Cr > Ni > Pb > Co > Cd > As. The results showed that metal levels in the primary feathers of waterbirds were greater than the other species of waterbirds examined across the world. Thus, the study emphasizes that managing wetlands and controlling pollution is crucial to saving waterbirds; otherwise, the population and diversity of waterbirds will decline and become a significant threat to waterbird communities.