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Trace metal concentrations were monitored in the yellow clam (Paphia malabarica), green mussel (Perna viridis) and edible oyster (Crassostrea madrasensis) from growing areas in the Ashtamudi and Vembanad estuaries, Kerala. Samples of shellfish (clams n=26, mussels n=18, oysters n=36) and environmental parameters (salinity, temperature, pH and rainfall) were measured in these growing areas from July 2012 to December 2014. Ranges of mean annual concentrations (mg/kg) were Ni (0.46-0.65); Co (2.87-3.49); Fe (80.0-119.4); Mn (3.88-9.38); Zn (40.8-76.2); Pb (1.28-2.00); and Cu (1.59-4.38). In Ashtamudi, clams had higher mean concentrations of Ni, Co, Fe, Mn and Pb than oysters. Mean concentrations of Ni, Pb (in all species), Zn (in clams and mussels) and Cu (in mussels) did not exceed maximum permissible limits mandated by the Food Safety and Standards Authority of India. Mean Mn concentrations exceeded the World Health Organization guideline (1 mg/kg) in the three species while mean Fe concentrations in clams and oysters did not exceed the guideline (100 mg/kg). Target hazard quotients were generally ≤ 1, except for a few Pb results in clams and mussels. Although results suggest no health risk to consumers for the reference doses, daily intakes and elements considered, regular monitoring of trace metals is recommended to maintain consumer protection given increasing anthropogenic and climatic pressures on the shellfish growing areas.