The rapid development of graphene-based nanotechnologies in recent years has drawn extensive attention in environmental applications, especially for water treatment. Three-dimensional graphene-based macrostructures (GBMs) have been considered to be promising materials for practical water purification due to their well-defined porous structure and integrated morphology, and displayed outstanding performance in pollutant abatement with easy recyclability. Three-dimensional GBMs could not only retain the intrinsic priorities of 2D graphene, but also emerge with extraordinary properties by structural manipulation, so rational design and construction of 3D GBMs with desirable microstructures are important to exploit their potential for water treatment. In this review, some important advances in surface modification (chemical doping, wettability, surface charge) and geometrical control (porous structure, oriented arrangement, shape and density) with respect to 3D GBMs have been described, while their applications in water purification including adsorption (organic pollutants, heavy metal ions), catalysis (photocatalysis, Fenton-like advanced oxidation) and capacitive desalination (CDI) are detailly discussed. Finally, future challenges and prospective for 3D GBMs in water purification are proposed.