Lead (Pb) is a globally significant priority contaminant in coastal and estuarine ecosystems, where continuous sediment-water exchange regulates its bioavailability and subsequent ecological risks. Intertidal biofilms, which function as major primary producers in estuarine ecosystems, are continuously exposed to Pb through sediment remobilization and water-column transport; however, the relative contribution of dissolved versus sediment-bound Pb to biofilm uptake and the mechanisms governing its subsequent fate remain poorly understood. In this investigation, intertidal biofilms from world’s largest tidal mangrove forest, the Indian Sundarbans, were used as a model system to investigate Pb behaviour and sequestration using an integrated laboratory sediment-water microcosm combining stable Pb isotope tracing, biogeochemical analyses, shallow-shotgun metagenomics and microscopic characterisation.