An acid leachable technique is employed in core samples (C1, C2 and C3) to develop a baseline data on the sediment quality for trace metals of River Uppanar, Cuddalore, southeast coast of India. Acid leachable metals (Fe, Mn, Cr, Cu, Ni, Co, Pb, Zn and Cd) indicate peak values at the sulphidic phase and enrichment of metals in the surface layers are due to the anthropogenic activities. Association of trace metals with Fe, Mn indicates their adsorption onto Fe-Mn oxyhydroxides and their correlation with S indicate that they are precipitated as metal sulphides. Factor analysis identified three possible types of geochemical associations and the supremacy of trace metals along with Fe, Mn, S and mud supports their geochemical associations. Factor analysis also signifies that anthropogenic activities have affected both the estuarine and fresh water regions of River Uppanar.