Water and intertidal sediment samples were collected from 28 stations along the Thames Estuary, from the tidal limit to the outer estuary. Surveys were conducted in 1997, 1999 and 2001 to assess spatial distributions and short-term variability. Highest concentrations of trace metals in water coincided with high turbidity in the mid-estuarine region, although the particle-associated fraction varied from 22% (As) to 95% (Pb). Theoretical dilution line (TDL) plots showed that dissolved metals were largely derived from a combination of diffuse (sediment desorption) and localised point sources (outfalls, industry). Dissolved Cu and Zn both exceeded environmental quality standard (EQS) levels during the survey period. The majority of sediment metals showed common distributional patterns, with increasing concentrations upstream. This increase was greatest for pollutant metals: Ag, Cd, Cu, Hg, Pb and Zn. Partial extraction of sediment metals with 1 M HCl showed that >50% of Ag, Cd, Cu, Mn, Pb and Zn were potentially bioavailable and that the proportion of bioavailable sediment metals also increased upstream. The majority of sediment metal concentrations exceeded Interim Sediment Quality Guideline threshold effects levels (TELs) over much of the estuary. Sediment concentrations of Cu, Hg, Pb and Zn also exceeded probable effects levels (PELs) at many estuarine sites. Despite improvements in recent years, the Thames Estuary remains chronically contaminated with a range of metals.