Mercury concentrations were investigated in freshwater sediment from two canals in Scotland, UK. High concentrations found in the Union Canal (35.3–1200 mg kg−1) likely originate from historical munitions manufacture, with lower levels in the Forth & Clyde Canal (0.591–9.14 mg kg−1). Concentrations of methylmercury (MeHg) were low – from 6.02 to 18.6 μg kg−1 (0.001–0.023% of total Hg) in the Union Canal and from 3.44 to 14.1 μg kg−1 (0.11–0.58% of total Hg) in the Forth & Clyde Canal – and there was a significant inverse relationship between total Hg concentration and %MeHg. Total Hg concentration was significantly negatively correlated with pH and positively correlated with Fe content (in the Union Canal only) but not with organic matter, S content or the proportion of clay present. The MeHg concentration was not correlated with any of the above sediment parameters. Ethylmercury was detected in the most highly contaminated sediments from the Union Canal.