•Accumulation of Hg in sediments is influenced by finer particles (silt and clay).•The increasing complexation/reduction processes of Hg by DOM decrease Hg sequestration.•TOC and DOM control sequestration of Hg by sediments. Total organic carbon (TOC) (in sediment) and dissolved organic matter (DOM) (in water column) play important roles in controlling the mercury sequestration process by the sediments from the central east coast of India. This toxic metal prefers to associate with finer size particles (silt and clay) of sediments. Increasing concentrations of DOM in overlying water column may increase complexation/reduction processes of Hg2+ within the water column and decrease the process of Hg sequestration by sediments. However, high concentrations of DOM in water column may increase Hg sequestration process by sediments.