Water governance is a complex process to manage and improve due to the large numbers of competing scales and levels inherent within it. Effectively supporting any water governance process does not just rely on hydrological knowledge of a water system, but much broader trans‐disciplinary understanding of a whole socialhydrological system. In this paper we show how there are commonly up to eight or more competing scales—spatial, temporal, administrative, institutional, management, network, knowledge/information and stakes/issues—present in any water governance situation. Processes in one scale can then create flows or externalities that produce multi‐level, cross‐scale or rescaling effects. A typology of six types of externalities or flows is provided—physical or material flows (e.g. water and solute movement), information and knowledge, political and social control, financial flows, human flows, and an irreversibility effect (e.g. flows, such as that of time passing, which lead to cumulative effects that are difficult or impossible to reverse)—and used to study the examples provided in the 15 papers of this special issue. From these insights, conclusions are drawn on how conflicts across competing scales are currently being managed, the mechanisms involved in bridging scales, and to what extent currently privileged scales and/or governance structures are appropriate for effectively managing water and land. The two general trends observed for multi‐level and cross‐scale management remain the need for collaborative governance processes and facilitators of these interactions, as well as the development of savvy coalitions for water governance change who understand and can effectively navigate these complex multi‐level and multi‐scalar systems. There is also a need to recognise that water basins or watersheds are social constructions and not always the most effective arenas for water governance. Problemsheds based on concepts such as the French “territoire” (territory), may in fact prove more pertinent in many cases (e.g. highly engineered systems) due to the unequivocal social nature of their construction and ability to delineate a range of agreed upon social‐hydrological systems for management.