The planetary boundaries framework defines the ‘safe operating space for humanity’ represented by nine global processes which can destabilize the Earth System if perturbed. The water planetary boundary attempts to provide a global limit to anthropogenic water cycle modifications, but it has been challenging to translate and apply it to the regional and local scales at which water problems and management typically occur. We develop a cross-scale approach by which the water planetary boundary could guide sustainable water management and governance at sub-global contexts defined by physical features (e.g. watershed or aquifer), political borders (e.g. city, nation, or group of nations), or commercial entities (e.g. a corporation, trade group, or financial institution). The application of the water planetary boundary at these sub-global contexts occurs via two approaches: (i) calculating fair shares, in which local water cycle modifications are compared to that context’s allocation of the global safe operating space, taking into account biophysical, socio-economic, and ethical considerations; and (ii) defining a local safe operating space, in which interactions between water stores and Earth System components are used to define local boundaries required for sustaining the local water system in stable conditions, which we demonstrate with a case study of the Cienaga Grande de Santa Marta wetlands in Colombia. By harmonizing these two approaches, the water planetary boundary can ensure that water cycle modifications remain within both local and global boundaries and complement existing water management and governance approaches.