Purpose Manchester is often heralded as the first industrial city. Large volumes of physical and liquid contaminants were released into its river network throughout the industrial period up to the latter part of the twentieth century. Water quality has improved dramatically in recent decades, but, given their environmental significance, it is important to ascertain the extent to which a legacy of contamination persists in the modern bed sediments. Materials and methods Fine-grained bed sediments were sampled at 40 sites in the Mersey and Irwell catchments. Sediments were wet sieved to isolate the <63-μm grain size fraction. Metal concentrations were determined using XRF. Particle size characteristics were also measured. Sediments were subjected to a five-step sequential extraction procedure to ascertain the environmental significance of metal concentrations. Alongside archival research of past industry, enrichment factors, multivariate statistical techniques and conditional inferences trees were used to identify sources of heavy metals. Results and discussion Bed sediment-associated heavy metal(loid) concentrations were as follows: As (9.89–110 mg kg−1), Cr (76.5–413 mg kg−1), Cu (53.1–383 mg kg−1), Pb (80.4–442 mg kg−1) and Zn (282–1020 mg kg−1). Enrichment factors ranged from moderate to extremely severe, with Pb showing the greatest enrichment across the catchments. Chemical mobility was generally low, but metal(loid) partitioning identified the influence of anthropogenic sources. Statistical analysis highlighted a number of point sources associated with former industrial sites that operated during the industrial period. Conditional inference trees highlighted the role of the textile industry on Cu concentrations in addition to indicating the complexity of sources, fluxes and stores of sediment-associated contamination throughout the system. Conclusions Fine-grained sediment-associated metal(loid)s in the Mersey and Irwell catchments are anthropogenically enriched. Concentrations also exceed sediment quality guidelines. A lack of distinct spatial patterning points to a complex network of contaminant inputs across the catchments, even in the headwaters. Whilst potential modern urban sources are likely to be important, spatial patterns and multivariate/data mining techniques also highlighted the importance of releases from former industrial sites as well as the reworking of historically contaminated floodplains and soils.