Environmental context. Determining associations between trace metals and nanoparticles in contaminated systems is important in order to make decisions regarding remediation. This study analysed contaminated sediment from the Clark Fork River Superfund Site and discovered that in the <1-µm fraction the trace metals were almost exclusively associated with nanoparticulate Fe and Ti oxides. This information is relevant because nanoparticles are often more reactive and show altered properties compared with their bulk equivalents, therefore affecting metal toxicity and bioavailability.Abstract. Analytical transmission electron microscopy (aTEM) and flow field flow fractionation (FlFFF) coupled to multi-angle laser light scattering (MALLS) and high-resolution inductively coupled plasma mass spectroscopy (HR-ICPMS) were utilised to elucidate relationships between trace metals and nanoparticles in contaminated sediment. Samples were obtained from the Clark Fork River (Montana, USA), where a large-scale dam removal project has released reservoir sediment contaminated with toxic trace metals (namely Pb, Zn, Cu and As) which had accumulated from a century of mining activities upstream. An aqueous extraction method was used to recover nanoparticles from the sediment for examination; FlFFF results indicate that the toxic metals are held in the nano-size fraction of the sediment and their peak shapes and size distributions correlate best with those for Fe and Ti. TEM data confirms this on a single nanoparticle scale; the toxic metals were found almost exclusively associated with nano-size oxide minerals, most commonly brookite, goethite and lepidocrocite.