The upper Spencer Gulf in South Australia hosts the world’s largest single stream Pb-Zn smelter, which has caused environmental and health issues related to elevated metal concentrations in the surrounding environment. The area also has extensive seagrass meadows, occupying N4000 km2 . We reconstructed the fluxes of heavy metals over the last ~3000 years through a multi-parameter study of the soil archives formed by the seagrass Posidonia australis. Pb, Zn and Cd concentrations increased up to 9-fold following the onset of smelter operations in the 1880s, and the stable Pb isotopic signatures confirmed the smelter has been the main source of lead pollution in the seagrass soils until present. Preliminary estimates suggest that over the past 15 years seagrass meadows within 70 km2 of the smelter accumulated ~7–15% of the smelter emissions in their soils. Here we demonstrate that seagrass meadows act as pollution filters and sinks while their soils provide a record of environmental conditions, allowing baseline conditions to be identified and revealing the time-course of environmental change.