Waterbirds may be a good indicator of harmful metal levels in aquatic environments. Waterbirds’ organs and tissues were tested for the presence of pollutants, such as metals. However, very few reports describe the use of bird feathers and their prey in metal analysis. In the present research, seven metals were measured in the tissue, kidney, liver, and feathers of the Indian pond heron, the black-crowned night heron, and their prey species, including crabs, prawns, molluscs, and fishes from a freshwater lake. Metals were examined using an ECIL-4141-double beam atomic absorption spectrophotometer (DB-AAS). Metal concentrations differed considerably in the tissue, kidney, liver, and feathers of the Indian pond heron and black-crowned night heron (p < 0.001). Indeed, this research discovered a good correlation between the metals of prey species and the tissues, kidneys, liver, and feathers of waterbirds that were tested. The regression model explained that the Cyprinus carpio influence the accumulation of metals about 98.2% in tissues, Macrobrachium rosenbergii and Cyprinus carpio around 86.3% in the kidney, the Labeo rohita almost 47.2% in the liver and Labeo rohita nearly 93.2% on the feathers of the Indian pond heron. On the other hand, the Mystus vittatus, Cyprinus carpio, Labeo rohita influence about 98.8% in tissue, the Claris batrachus and Tilapia mossambica around 93.3% in kidney, the Mystus vittatus, Cyprinus carpio, about 93.2% in liver and the freshwater crab (Travancoriana schirnerae), freshwater prawn (Macrobrachium rosenbergii) and a fish (Cyprinus carpio) nearly 93.2% in feathers in the black-crowned night heron. This research evaluated metals in the dead carcasses of waterbirds, a non-invasive biomonitoring technique for pollution. Overall, the investigation revealed that the lake is severely contaminated with metals. Therefore, the management and protection of aquatic habitats, particularly freshwater lakes, should be enhanced to rescue wild species that rely on aquatic ecosystems and to ensure that people have access to clean drinking water.