We bring together two decades of research on cross-scale spatial and temporal connectivity of water in the Anthropocene to understand the implications for institutional fit and water governance, with a focus on river basin organizations and watershed-based bodies. There is strong evidence showing how hydrological cycles are tightly coupled across larger spatial scales than they were in the past, which implies a possible expansion of the boundaries typically considered in the study and governance of water. Temporally, frequent time lags between action and consequence and the potential for increasing concurrence of extreme events pose risks for decision-makers trying to make accurate and appropriate decisions. Both cross-scale spatial and temporal connectivity create new challenges to key principles regarding participation, deliberation and collaboration in water governance. We argue for a shift from emphasizing how governance can ‘fit’ a closed, biophysical boundary towards a stronger consideration of institutional ‘fitness’ through flexibility, responsiveness and anticipatory capacity to better support water resilience and sustainability.