Existing toxicity data indicate that industrial-scale production of C60 fullerene poses a potential threat to the environment. Evaluating the environmental impact of C60 requires careful characterization of its physicochemical properties in the natural aqueous environment. Our study aims to determine the effects of aquatic natural organic matter (NOM) on the physicochemical properties of aqueous C60 nanoparticles, nC60. Stable nC60 suspensions were formed using three different solvent exchange protocols. They were thoroughly characterized for particle size, morphology, and electrophoretic mobility in the absence or presence of two model NOM components, Suwannee River humic acid and fulvic acid. NOM caused disaggregation of nC60 crystals and aggregates under typical solution conditions of natural water, leading to significant changes in particle size and morphology. Such effect increased with increasing NOM concentration. The changes in nC060 size and morphology strongly depended on the nC60 formation pathway. Results from this study indicate that NOM may play a critical role in the transport and toxicity of C60 in the natural aqueous environment.