Nested fullerenes display a range of unique properties influenced by their size and shape. In this paper, the size- and shape-dependent aggregation of nested fullerenes in water is studied using explicit solvent molecular dynamic simulations. It is shown that water forms a layered structure near the surface of the particle, with the density of interfacial water increasing with increasing particle size. Meanwhile, water molecules near the extended facets of large nested fullerenes are unable to maintain their hydrogen bonding network, leading to a shape and size mediated structuring of surrounding waters. These distortions affect the overall association kinetics of particles in water with spherically shaped particles transitioning quickly into contact, while larger fullerenes, characterized by a lower sphericity, cluster at a much slower rate.