Agricultural expansion and intensification have altered the quantity and quality of global water flows. Research suggests that these changes have increased the risk of catastrophic ecosystem regime shifts. We identify and review evidence for agriculture-related regime shifts in three parts of the hydrological cycle: interactions between agriculture and aquatic systems, agriculture and soil, and agriculture and the atmosphere. We describe the processes that shape these regime shifts and the scales at which they operate. As global demands for agriculture and water continue to grow, it is increasingly urgent for ecologists to develop new ways of anticipating, analyzing and managing nonlinear changes across scales in human-dominated landscapes.