Nanoparticulates released from surface soils may significantly affect contaminant fate and transport. Here, we show that nanoscale soil particles can markedly enhance the transport of BDE-209 (one of the most commonly detected polybromodiphenyl ethers (PBDEs) in the environment) in groundwater. Specifically, BDE-209 that is initially associated with three types of soil nanoparticles—including nanoparticles extracted from black soil (Mollisol), purple soil (Inceptisol), and loess soil (Entisol)—remains bound to the nanoparticles when migrating through saturated porous media, regardless of the types of surface coating and heterogeneity (i.e., quartz sand, humic-acid-coated sand, and goethite-coated sand). Accordingly, the mobility of BDE-209 is determined by the mobility of the soil nanoparticles. The nanoparticles of black soils have the highest mobility, whereas those of loess soil display the lowest mobility, because the presence of calcite enhances the deposition of the nanoparticles due to increased particle aggregation and ripening. The coating of humic acid on quartz sand enhances the mobility of all three soil nanoparticles (and therefore, BDE-209) due to increased electrostatic repulsion, steric hindrance, and the blocking of deposition sites, while the coating of goethite subdues the mobility due to decreased electrostatic repulsion and deposition in the primary minimum (i.e., positively charged surface heterogeneity). Findings in this study highlight the important roles of soil nanoparticles in mediating contaminant behaviors and point to the potential risks of PBDE spreading in groundwater, even though the common wisdom is that these chemicals are highly immobile and PBDE contamination is restricted to surface soils.