The present study aims to assess the extent of trace metal pollution in the sediments of Sita-Swarna estuary, west coast of India, and investigate their possible ecological risk on the aquatic environment. The sediment cores were analyzed for sand, silt, clay, organic carbon, and trace metals (Al, Fe, Mn, As, Cd, Co, Zn, Pb, Ni, Cr, and Cu) at 2-cm intervals. The study revealed that sediments have deposited in relatively violent to very violent hydrodynamic energy conditions. Factor analysis indicated that the metal distribution is mainly controlled by Fe–Mn oxyhydroxides and organic carbon. Further, the geochemical approach, pollution indices, and statistical evaluation revealed moderate pollution in the catchment. From an ecotoxicological perspective, the estimated risk index (RI) value was found to less than 150, indicating low risk for aquatic life. Thus, this baseline study would help to adopt strategies in pollution control and protect the fragile marine environment.