This paper seeks to relate strategic themes in water resources management to the practicalities of imposing particular regulatory measures on water uses and to protect aquatic ecosystems. Specifically, a contrast is drawn between the global imperative of Integrated Water Resources Management (IWRM) and the sectoral (issue-by-issue) approach to water regulation that has traditionally prevailed in both regional (EU) and national legislation. The intuitive attractions of ‘integration’ are contrasted with the challenges of interrelating this to the diverse purposes for which water legislation is adopted, both for human needs and for ecological purposes. These challenges are well illustrated in the EU Water Framework Directive (WFD) which purports to adopt an ‘integrated’ approach, but is actually concerned with water quality, largely to the exclusion of other water-related concerns. Insofar as the Directive does seek to secure integration between water quality and water quantity concerns in surface water, this is only done in a secondary or incidental way. Water flow becomes relevant only where specified environmental objectives under the Directive are not being met. However, the legally contingent status of flow has been bolstered markedly by recent guidance on ecological flows under the WFD Common Implementation Strategy. The significance of this guidance is discussed and related to the implementation challenges that it raises. In relation to the UK, and particularly England, it is argued that the response to addressing water flow issues arising under the WFD had been dilatory and inadequate. Concluding observations reflect on the global, regional and national challenges to integration of water legislation as they have been illustrated by the discussion of regulating for ecological water flows.