Fullerene-based nanomaterials (FNMs) are emerging in a variety of potential applications, including cosmetics, energy production, semiconductors, and medical treatments. Properties of nanomaterial suspensions are typically summarized by average values for the purposes of characterizing these materials and interpreting experimental results. However, this work shows that the heterogeneity in aqueous suspensions of fullerene C60 aggregates (nC60) must be taken into account for the purposes of predicting nanomaterial transport, exposure, and biological activity. The production of reactive oxygen species (ROS), microbial inactivation, and the mobility of the aggregates of the nC60 in a silicate porous medium all increased as suspensions were fractionated to enrich with smaller aggregates by progressive membrane filtration. These size-dependent differences are attributed to an increasing degree of hydroxylation of nC60 aggregates with decreasing size. Also, the presence of humic acid and salts increased size of aggregates and decreased ROS generation. As the quantity and influence of these more reactive fractions may increase with time, experiments evaluating fullerene transport and toxicity end points must take into account the evolution and heterogeneity of fullerene suspensions.