The authors examine the complex history of the development of the Indus Basin and the challenges faced by Pakistan during the evolution of the Indus Basin Irrigation System and the country's responses to date. The Indus river system must meet the multiple needs of agriculture, energy and flood security. Pakistan's constitutional structure, in which the federation shares overall responsibility for the operation of the Indus with the provinces, poses unique management and implementation challenges. What are the institutional arrangements Pakistan needs to address the challenges to the Indus Waters Treaty it signed with India in 1960? How is the country going to regulate the use of over-abstraction in the basin with the increased reliance on groundwater to maintain agricultural productivity? What are the institutional mechanisms in place to manage increased river flow variations from glacial melt as a result of climate change and for coping with devastating floods? At the same time, is the country maintaining adequate environmental flows to its delta? Provincial mistrust and a lack of institutional capacity underpins the history of the Indus in Pakistan with the Interprovincial Water Accord 1991 serving as a ray of hope on which to build a new institutional architecture of cooperation.