Applications of graphene sheets in the fields of biosensors and biomedical devices are limited by the aqueous solubility of graphene. Consequently, understanding the role of water molecules in the aggregation or dispersion of graphene in aqueous solution with a biomolecule is of vital importance to its application. Herein, protein is spontaneously released by the layer-to-layer aggregation of two single-layer graphene sheets due to van der Waals force between the sheets. The properties of water molecules, including density and dynamics, are discussed in detail. The dynamic behavior of aggregation of graphene sheets is triggered by the dynamics of water molecules. To stabilize dispersed graphene sheets in aqueous solution, the density of water molecules between the graphene sheets should be larger than 0.83 g cm−3, and graphene modified by hydroxyl groups could be a good choice. The stability of a model protein on the graphene sheet is studied to investigate the biological compatibility of graphene sheets. To be a material with good biocompatibility, graphene should be functionalized by hydrophilic groups. The results presented herein could be helpful in the research and application of graphene sheets in the fields of biomaterials, biosensors, and biomedical devices.