Nanominerals and mineral nanoparticles from a mining-contaminated river system were examined to determine their potential to co-transport toxic trace metals. A recent large-scale dam removal project on the Clark Fork River in western Montana (USA) has released reservoir and upstream sediments contaminated with toxic trace metals (Pb, As, Cu and Zn), which had accumulated there as a consequence of more than a century and a half of mining activity proximal to the river’s headwaters near the cities of Butte and Anaconda. To isolate the high-density nanoparticle fractions from riverbed and bank sediments, a density separation with sodium polytungstate (2.8 g/cm3) was employed prior to a standard nanoparticle extraction procedure. The stable, dispersed nanoparticulate fraction was then analyzed by analytical transmission electron microscopy (aTEM) and flow field-flow fractionation (FlFFF) coupled to both multi-angle laser light scattering (MALLS) and high-resolution, inductively coupled plasma mass spectrometry (HR-ICPMS). FlFFF analysis revealed a size distribution in the nano range and that the elution profiles of the trace metals matched most closely to that for Fe and Ti. aTEM confirmed these results as the majority of the Fe and Ti oxides analyzed were associated with one or more of the trace metals of interest. The main mineral phases hosting trace metals are goethite, ferrihydrite and brookite. This demonstrates that they are likely playing a significant role in dictating the transport and distribution of trace metals in this river system, which could affect the bioavailability and toxicity of these metals.