The Mandovi Estuary, located along the tropical west coast of India, transforms from being a freshwater-dominated body during the monsoon season to a tide-dominated system during post-monsoon season, with a salinity gradient developing from the freshwater end to the estuarine mouth (∼0–33). The sulphate reduction (SR) rates were measured by the 35SO42− radiotracer method in the estuarine sediments at three different sites. The porewater H2S concentrations were negligible at all the sites and SR rates did not exhibit any clear trend along the salinity gradient. Pyrite content (3.45–12.9 mg g−1) was the highest at the marine end and decreased towards the freshwater end. The SR rate (15.71 mmol m−2 d−1) and total Fe content (14–20%) were highest in sediments of mid-estuary with intermediate salinity and variable porosity. Organic carbon (OC) mineralization rate through SR also did not show any trend along the salinity gradient with intermediate salinity site having higher values (31.83 mmol C m2 d−1) compared to other sites (3.12–8.62 mmol C m2 d−1). SR was responsible for ∼8–50% of sedimentary OC mineralization implying that OC mineralization through Fe (III) and Mn (IV) reduction possibly played major role owing to their high concentrations in the estuarine sediments.