Three-dimensional macrostructures (3DMs) of graphene and graphene oxide are being developed for fast and efficient removal of contaminants from water and air. The large specific surface area, versatile surface chemistry and exceptional mechanical properties of graphene-based nanosheets enable the formation of robust and high-performance 3DMs such as sponges, membranes, beads and fibres. However, little is known about the relationship between the materials properties of graphene-based 3DMs and their environmental performance. In this Review, we summarize the self-assembly and environmental applications of graphene-based 3DMs in removing contaminants from water and air. We also develop the critical link between the materials properties of 3DMs and their environmental performance, and identify the key parameters that influence their capacities for contaminant removal.