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Surface sediments (n ¼ 85) from a 160-km river-estuarine transect of the Clyde, UK, were analysed for total mercury (Hg), saturated hydrocarbons and unresolved complex mixtures (UCMs) of hydrocarbons. Results show that sediment-Hg concentration ranges from 0.01 to 1.38 mg kg–1 (mean 0.20 mg kg–1) and a spatial trend in Hg-content low–high–low–high, from freshwater source, to Glasgow, to estuary, is evident. In summary, sediment-Hg content is low in the upper Clyde (mean of 0.05 Hg mg kg–1), whereas sediments from the Clyde in urbanised Glasgow have higher Hg concentrations (0.04 to 1.26 mg kg–1; mean 0.45mgkg–1), and the inner estuary sediments contain less Hg (mean 0.06 mg kg–1). The highest mean sediment Hg (0.65 mg kg–1) found in the outer estuary is attributed to historical anthropogenic activities. A significant positive Spearman correlation between Hg and total organic carbon is observed throughout the river estuary (0.86; P < 0.001). Comparison with Marine Scotland guidelines suggests that no sites exceed the 1.5 mg kg–1 criterion (Action Level 2); 22 fall between 0.25 and 1.5 mg kg–1 dry wt. (Action Level 1) and 63 are of no immediate concern (<0.25 mg kg–1 dry wt.). Saturated (n-alkane) hydrocarbons in the upper Clyde are of natural terrestrial origin. By contrast, the urbanised Glasgow reaches and outer estuary are characterised by pronounced and potentially toxic UCM concentrations in sediments (380–914 mg/kg and 103–247 mg kg–1, respectively), suggesting anthropogenic inputs such as biodegraded crude oil, sewage discharge and/or urban run-off.