Integrated water resource management (IWRM) is widely accepted and has been implemented though international, national and regional water management guidelines. Nonetheless, concrete implementation of IWRM gives rise to new questions for policy analysis. Scholars interested in water regulation, the design of effective and efficient policy instruments, and structures of participative and multi‐level policy processes face challenges regarding research design, concepts and empirical approaches. This special issue integrates research about regional, national and transboundary policy perspectives on water management in seven countries, four continents and two transnational water bodies. From the six articles presented in this special issue, we learn more about how to define integration, to think about borders and scales and to theoretically and empirically study collaborative management in water policy analysis. Copyright © 2016 John Wiley & Sons, Ltd and ERP Environment