Mangrove forests sequester organic carbon, nutrients and toxic metals sorbed to fine sediment, and thus restrict the mobility of pollutants through estuarine environments. However, mangrove removal and environmental degradation caused by industrial activity and urban growth can impact the ability of mangrove communities to provide these critical ecosystem services. Here, we use sediment profiles from an impacted tropical estuary in southwest India to provide a c. 70-year record of carbon, nutrient and trace metal burial in the context of rapid urban development and the systemic removal of mangrove communities. Our results show that carbon and nutrient accumulation rates increase sharply during the 1990's in accordance with the high rates of deforestation. Nitrogen and phosphorus accumulation rates increased fourfold and twofold, respectively, during the same period. Organic carbon accumulation was fivefold higher than the global average during this period, reflecting intense deforestation during the last three decades. The enrichment of Hg, Zn, Pb, Mo, Ni, Cu and Mn demonstrate clear anthropogenic impact starting in the 1950's and peaking in 1990. Mercury, the trace metal with the highest enrichment factor, increased sevenfold in the most recent sediments due to increased fossil fuel emissions, untreated water and incineration of medical waste and/or fertilizers used in aquaculture. Organic carbon isotope (δ13C) and C:N molar ratios indicate shifts to more terrestrial-derived source of organic matter in the most recent sediments reflecting growing deforestation of which may be prevalent in southeast Asia due to increasing development. This study emphasizes the critical role played by mangrove ecosystems in attenuating anthropogenically-derived pollutants, including carbon sequestration, and reveals the long-term consequences of mangrove deforestation in the context of rapidly developing economies. Display omitted •Mercury enrichment has increased up to 7-fold since the 1950's.•Increasing carbon burial in a tropical estuary is related to deforestation.•Recent sediments show high rates of carbon and nutrient burial.•Tropical mangroves are important sinks for pollutants in areas of rapid development.