With widespread production and use of C60 fullerene nanoparticles, their release to the environment and natural waters is inevitable. The colloidal nature of C60 fullerene in the aquatic environment significantly influences its behavior in the environment including its transport, bioavailability and toxicity to different organisms. Natural organic matter (NOM) is a ubiquitous and reactive material in aquatic environments with significant structural heterogeneity. Therefore, the effect of NOM molecules on the colloidal behavior of fullerene particles needs to be studied. A major part of NOM consists of humic acids (HA). HAs have pronounced effects on the aggregation of C60 fullerene in water. The Has were sequentially extracted from compost. The structure of extracted HAs became increasingly aliphatic and hydrophobic with increasing number of extractions. Molecular weights of HAs and their affinity for adsorbing simple nonpolar molecules from water also increased with increasing number of extractions. The effect of HAs, fulvic acid (FA) and tannic acid (TA) on aggregation behavior of C60 fullerene suspension (nC60) was investigated. Aggregation was started by addition of varying amounts of Ca2+ to the nC60 with 2 mg/L of each type of NOM. The absolute value of the zeta potential |ζ| of pure nC60 increased after the addition of any type of NOM. Addition of Ca2+ to the (nC60 + NOM) system decreased |ζ| of fullerene almost uniformly for all types of NOM. The nC60 critical coagulation concentration (CCC) was equal to 14.5, 6.5, 5.4, and 3.7 mM Ca2+ for HA7, HA1, FA, and TA respectively. A nearly constant ζ for (nC60 +NOM) system across a wide range of Ca2+ concentrations suggested steric stability of the aggregates. Then the feasibility of nC60 removal from water sources with commonly used coagulants was investigated. Results showed that C60 could be removed with 80% efficiency at an optimum Al3+ dose. Divalent anions, such as CO32-, SO42-, HPO42- and humic acid (HA) could act as a bridge to connect C60-Al (OH)n(m-δ)+ particles together and induce the formation of flocs. This study highlighted the role of NOM on the transportation, aggregation, precipitation and fate of C60 fullerenes, when they enter the natural waters.