Port Jackson (Sydney Harbour) is a major deep-water estuary on the central New South Wales coast and is surrounded by a highly urbanised and industrialised catchment. Concentrations of trace metals and organochlorine pesticide residues are high in sediment in the upper reaches of the estuary. Historical fluxes of contaminants into the estuary were determined by radio-isotopic dating of 12 sediment profiles in nine highly contaminated embayments. The onset of contamination in estuarine sediment was correlated with catchment-wide urbanisation and industrialisation of Sydney. Contamination of estuarine sediment in Port Jackson first occurred ca 1860, near the present central business district and spread westward and northward. Trace-metal contamination was initiated ~20 years after the commencement of industry in the subcatchments, and a rapid increase in trace-metal concentrations corresponds closely with maximum industrial activity in these catchments. Organochlorine pesticide residues occur in estuarine sediments 40-50 years after the onset of contamination by trace metals and their appearance closely corresponds with the manufacturing and application history of these compounds. The transit time of contaminants from fluvial catchment to incorporation in estuarine sediment is short (probably <2 years). Trace metals in sediment reached maximum concentrations in 1970 and a subsequent decrease in concentrations in the upper estuary reflects relocation of industry away from the estuary foreshores and tighter controls on industrial discharges. In Middle Harbour and the lower estuary, trace-metal concentrations continue to increase, due to the comparatively recent increases in commercial and industrial growth in these areas.