This study quantifies the abundances of 52 elements in the surface sediments of Muttukadu Estuary, India, to determine the potentially toxic elements (PTEs) contamination and their partition into different phases in the sediments. Various pollution assessment parameters (enrichment factor, contamination factor, and geo-accumulation Index) confirm significant pollution concerning As, Se, Mo, Cd, Pb, Bi, Th, U, and P, and moderate pollution in Cu and Zn. The pollution load index values indicate high metal pollution in eight locations, with a majority close to a man-made canal, indicating contribution from anthropogenic sources. Results of the sequential extraction reveal a higher risk of metals, particularly, Cu, As, Se, Mo, and Cd that are enriched in the non-lithogenic phases (dominantly organic-bounded) compared to the residual phase. High Cd (11%) and Mo (4%) bounded to the soluble-exchangeable phase could be related to the higher ability of principal polarization. The Potential Ecological Risk Index and Risk Assessment Code reveal a high risk of Cd and a significant risk of many other metals to the ecosystem, particularly at locations within the canal. Principal component analysis and cluster analysis reveal two major sources of metal pollution, attributed to anthropogenic (industrial/municipal discharge and recreational activities in the lake) and geogenic sources as well as the bioaccumulation process.