On 26th December (Boxing Day) 2015 an exceptional flood event occurred in the Irwell catchment, UK, whilst the neighbouring Mersey catchment experienced a much more typical winter runoff event. This provided an opportunity to examine the influence of high magnitude hydrological processes on the behaviour of fine‐grained metal‐contaminated bed sediments. Forty sites across the two catchments were sampled for channel bed fine sediment storage and sediment‐associated metal (loid) concentrations prior to, and following, the flooding. Sediments were analysed for total As, Cr, Cu, Pb, and Zn, and then subjected to a 5‐step sequential extraction procedure. Despite a significant reorganisation of fine‐grained (<63 μm) sediment storage, metal (loid) concentrations demonstrated markedly conservative behaviour with no significant difference observed between pre‐ and post‐flooding values across both catchments. Estimates of the channel bed storage of sediment‐associated metal (loid) s also showed minimal change as a result of the flooding. The metal partitioning data reveal only minor changes in the mobility of bed sediment‐associated metal (loid) s, indicating that such flood events do not increase the availability of sorbed contaminants in these catchments. Post‐flooding bed sediment metal (loid) loadings remain high, indicating persistent and long‐lasting sources of contamination within the Irwell and upper Mersey fluvial network.