Water dispersive 2D and 3D suprastructures offer a large number of potential applications in energy release, biomedicine and other fields. The nanomechanical properties of two suprastructures of self-assembled 9.6 nm Fe3O4 hydrophobic nanocrystals dispersed in water are elucidated by using atomic force microscopy. These suprastructures are either a shell consisting of a few layers of nanocrystals or spherical self-assemblies of nanocrystals in fcc superlattices called colloidosomes and supraballs, respectively. The major difference in the preparation of these suprastructure is based on the presence or not of octadecene molecules. It is recently demonstrated that these structures behave as nanoheaters and remain self-assembled after internalization in cancer cells. The observed differences between these suprastructures in terms of cell sensing are suggested to be related to their mechanical properties, which emphasize the importance of better understanding the nanomechanics of such suprastructures. In this study the nanomechanical properties of these suprastructures are shown to be load-depended in aqueous medium. Colloidosomes demonstrate higher flexibility and deformability than the supraballs. These findings provide essential knowledge for understanding differences in cell internalization and implementation in biomedicine. The differences in nanomechanical properties between these types of suprastructures are mainly due to their structures (hollow core–shell or fcc supracrystals).