Spatial patterns of land surface and subsurface characteristics often exert significant control over hydrological processes at many scales. Recognition of the dominant controls at the watershed scale, which is a prerequisite to successful prediction of system responses, will require significant progress in many different research areas. The development and improvement of techniques for mapping structures and spatiotemporal patterns using geophysical and remote sensing techniques would greatly benefit watershed science but still requires a significant synthesis effort. Effective descriptions of hydrological systems will also significantly benefit from new scaling and averaging techniques, from new mathematical description for spatial pattern/structures and their dynamics, and also from an understanding and quantification of structure and pattern-building processes in different compartments (soils, rocks, and land surface) and at different scales. The advances that are needed to tackle these complex challenges could be greatly facilitated through the development of an interdisciplinary research framework that explores instrumentation, theory, and simulation components and that is implemented in a coordinated manner.