•Physico-chemical parameters of water column control Hg speciation in sediments.•Sediments from the middle of the estuary were contaminated by Hg.•Concentrations of Hg were less during the monsoon and post monsoon period.•Salinity, pH of water column may change Hg speciation of the bottom sediments.•TOC in sediments control Hg partitioning in the system. Distribution and speciation of mercury (Hg) in the sediments from a tropical estuary (Godavari estuary) was influenced by the changing physico-chemical parameters of the overlying water column. The sediments from the upstream and downstream of the estuary were uncontaminated but the sediments from the middle of the estuary were contaminated by Hg. The concentrations of Hg became considerably less during the monsoon and post monsoon period. Total Hg concentrations and its speciation (at the middle of the estuary) were dependent on the salinity of the overlying water column. However, salinity had little or no effect on Hg association with organic phases in the sediments at downstream. Increasing pH of the overlying water column corresponded with an increase in the total Hg content in the sediments. Total organic carbon in the sediments played an important role in controlling Hg partitioning in the system. Uncomplexed Hg binding ligands were available in the sediments.