Perylene bisimides are among the most valuable functional dyes and have numerous potential applications. As a result of their chemical robustness, photostability, and outstanding optical and electronic properties, these dyes have been applied as pigments, fluorescence sensors, and n-semiconductors in organic electronics and photovoltaics. Moreover, the extended quadrupolar π system of this class of dyes has facilitated the construction of numerous supramolecular architectures with fascinating photophysical properties. However, the supramolecular approach to the formation of perylene bisimide aggregates has been restricted mostly to organic media. Pleasingly, considerable progress has been made in the last few years in developing water-soluble perylene bisimides and their application in aqueous media. This Review provides an up-to-date overview on the self-assembly of perylene bisimides through π–π interactions in aqueous media. Synthetic strategies for the preparation of water-soluble perylene bisimides and the influence of water on the π–π stacking of perylene bisimides as well as the resulting applications are discussed.