Graphene-based nanostructures and nanomaterials have been widely used for the applications in materials science, biomedicine, tissue engineering, sensors, energy, catalysis, and environmental science due to their unique physical, chemical, and electronic properties. Compared to two-dimensional (2D) graphene materials, three-dimensional (3D) graphene-based hybrid materials (GBHMs) exhibited higher surface area and special porous structure, making them excellent candidates for practical applications in water purification. In this work, we present recent advances in the synthesis and water remediation applications of 3D GBHMs. More details on the synthesis strategies of GBHMs, the water treatment techniques, and the adsorption/removal of various pollutants from water systems with GBHMs are demonstrated and discussed. It is expected that this work will attract wide interests on the structural design and facile synthesis of novel 3D GBHMs, and promote the advanced applications of 3D GBHMs in energy and environmental fields.