Desalination technologies, which remove solutes from water, are essential to the purification of water for agricultural and industrial purposes and for potable use. While a variety of desalination technologies exist, their performance and durability need improvements to meet future clean water demands. This challenge is particularly complex as a variety of feed water sources exists, which contain various amounts of salt, dissolved organic matter, suspended particulates, and other contaminants. Hence, predictive knowledge of the underlying physics and chemistry at the atomic and molecular scale is crucial for designing improved desalination materials and processes. In this Perspective, we outline how advanced characterization techniques, including X-ray, neutron, electron-based, and positron-based methods can be advantageously applied to water desalination technologies to provide detailed molecular insight, especially when combined with computational modeling. We summarize some of the scientific challenges in two prominent desalination techniques, membrane reverse osmosis and capacitive deionization, and lay out some specific approaches toward solving these challenges. With these developments, we anticipate that the use of advanced characterization can help advance the field of water desalination in much the same way that these have aided progress in energy storage and conversion science over the last decades.