Chilka lake, the largest coastal lagoon of Asia is one of the most dynamic ecosystems along the Indian coast. Historically the lagoon has undergone a considerable reduction in surface area due, in part, to input from natural processes but mostly due to human activities. The purpose of this investigation is to document the heavy metals' affinity for specific geochemical phases in the recently deposited sediments in the lagoon. Thirty-three samples were collected and analyzed for different geochemical phases of Fe, Mn, Cu, Cr, Ni, Pb, and Zn utilizing a sequential extraction scheme. In the nonlithogenous fraction, the exchangeable fraction was not geochemically significant, having <2% of the total metal concentration for all the elements. However, the carbonate fraction contained the following percentages of the total concentration: < 1% Fe, 13% Mn, 6% Cu, 4% Cr, 8% Ni, 13% Pb, and 12% Zn, suggesting the detrital origin of the sediments. Reducible and organic matter-bound fractions were the significant phases in the nonlithogenous fraction, containing 9% Fe, 16% Mn, 15% Cu, 16% Cr, 16% Ni, 14% Pb, and 14% Zn in the former and 4% Fe, 3% Mn, 17% Cu, 3% Cr, 14% Ni, 15% Pb, and 14% Zn in the latter. The phenomenon has been attributed to the scavenging affinity of Fe-Mn oxides and affinity for sorption into organic matter of the lagoon sediments. The lithogenous, residual fraction generally considered as a guide for natural background values was determined to contain 87% Fe, 67% Mn, 61% Cu, 77% Cr, 61.3% Ni, 56% Pb, and 60% Zn of the total concentrations.