Fifty six sediment cores were collected along a 100 km longitudinal transect of the Thames estuary. Total Hg ranged from 0.01 to 12.07 mg/kg, with a mean of 2.10 mg/kg (n=351). Concentrations of the toxic metal decreased downstream from London to the outer estuary and were positively correlated to total organic carbon (TOC) content. Many Hg profiles showed a clear rise, peak and fall, reflecting changing anthropogenic input through time. Surface concentrations averaged 1.27 mg/kg, confirming the effectiveness of recent environmental legislation and improved river management. Sediments at >40 cm depth from London reaches of the river (Waterloo Bridge, Cuckolds Point (Rotherhithe), Butlers Wharf (Tower Bridge), Millwall, Deptford and Millennium Dome) were highly contaminated, with levels of Hg of >7 mg/kg. The outer Thames had lower Hg, with the exception of Rainham, Crossness and Cliffe. Benchmarking against UK guidelines for the disposal of dredged material revealed that 88 samples from 21 sites exceeded the 3 mg/kg criteria (unsuitable for disposal at sea); 173 fell between 0.3 and 3 mg/kg (further assessment required); and 90 were of no concern. Using Hg as a generic pollution marker, the tidal Thames is one of the world's most contaminated river–estuarine sediment systems.