Increasing production and use of fullerene-based nanomaterials is likely to result in their environmental dispersal and subsequent human and ecosystem exposures. A thorough understanding of fullerene transport in the subsurface is essential to assessing environmental fate of fullerenes. To date, few transport studies have used actual environmental media or fullerene derivatives. In this study, the transport of two fullerene nanoparticles (i.e., aqueous colloidal suspensions of C60 [aqu/C60] and more water-soluble C60 derivative [C60 pyrrolidine tris-acid]) was studied in columns packed with model porous media (Iota quartz and Ottawa sand) and a sediment from Call’s creek under saturated and unsaturated steady-state flows. Fullerene retention was correlated with the degree of grain surface chemical heterogeneity manifested in amorphous Al hydroxide concentrations of the three media. Surface roughness was also responsible for the greatest fullerene retention in the sediment. As explained by the XDLVO theory, water soluble C60 PTA was more transported than aqu/C60 at near neutral pH, as results of its greater hydrophilicity and smaller particle sizes. Fullerene retention was dependent on solution pH and soil water saturation degree, and underlying mechanisms were discussed.