Three-dimensional (3D) graphene-based composite materials (3D GBCMs) have emerged as promising candidates for addressing critical challenges in water pollution remediation. This review selectively highlights the recent advancements in the application of 3D GBCMs to remove a wide range of contaminants, including heavy metals, dyes, salts, and pharmaceutical residues, from water. They owe their efficacy to their large surface area, interconnected porous structure, and functionalization potential. Three-dimensional GBCMs are promising materials for water filtration, offering capabilities such as heavy metal ion adsorption, the photocatalytic degradation of organic pollutants, and advanced desalination techniques like capacitive deionization (CDI) and solar desalination, thus providing sustainable solutions for obtaining freshwater from saline sources. Additionally, the factors influencing the pollutant removal capacities of 3D GBCMs, such as their material morphology, particle size, and porosity, are briefly discussed. Notably, the effect of the particle size on pollutant removal has not been extensively studied, and this review addresses that gap by exploring it in detail. Future research directions are also proposed, emphasizing the optimization and broader application of 3D GBCMs in environmental remediation. This review aims to provide valuable insights into the design and practical implementation of 3D GBCMs, offering guidance for their continued development in sustainable water treatment.