Desalination of seawater and brackish water is becoming an increasingly important means to address the scarcity of fresh water resources in the world. Decreasing the energy requirements and infrastructure costs of existing desalination technologies remains a challenge. By enabling the manipulation of matter and control of transport at nanometer length scales, the emergence of nanotechnology offers new opportunities to advance water desalination technologies. This review focuses on nanostructured materials that are directly involved in the separation of water from salt as opposed to mitigating issues such as fouling. We discuss separation mechanisms and novel transport phenomena in materials including zeolites, carbon nanotubes, and graphene with potential applications to reverse osmosis, capacitive deionization, and multi-stage flash, among others. Such nanostructured materials can potentially enable the development of next-generation desalination systems with increased efficiency and capacity.