International water institutions worldwide consider integrated water resources management (IWRM) to be the most sustainable way to manage water. Governments have modified their legal and institutional framework in order to apply integrated water management tools in the river basin. Institutional challenges are common in federations due to complex power sharing at national and subnational levels. This article discusses the implementation of the hegemonic model of IWRM in federations, based on a review of the literature for two different federal countries: Brazil and Switzerland. Due to the centralized character of Brazilian federalism, adjustments made in recent decades aimed to adapt the water management model through a hegemonic approach of participation and decentralization, shaped by international experiences and institutions. Some challenges concern vertical interplay, concerning coordination between levels and effective implementation of decentralization and participation. In contrast, Switzerland has a non-hegemonic model of water management, which is varied and fragmented throughout the country. As management is decided and applied locally, the main challenge concerns horizontal interplay, with regionalization and coordination of water uses.