What are the primary threats to freshwater resources worldwide?  A freshwater ecologist might say that water withdrawals, river fragmentation, non-native species introductions, and water pollution greatly imperil freshwater resources.  However, according to the United Nations, widespread poverty, malnutrition, growing urbanization, globalization, and climate change are principal factors that impact freshwater systems and management of water resources.  The framework of integrated water resources management (IWRM) offers a space to effectively address these intertwined issues and facilitate collaboration between freshwater scientists and water resource managers.  IWRM is an applied process now receiving strong political and legal backing internationally as a means for meeting human water needs in an equitable and efficient manner without causing unacceptable degradation to freshwater ecosystems.  In the Pastaza River Basin, an Andean-Amazon catchment (Ecuador/Peru), an IWRM approach is being implemented to address threats to freshwater biodiversity and human health resulting from water pollution.  In the Mara River Basin of eastern Africa (Kenya/Tanzania), IWRM is being applied as a means for securing sufficient water for humans and the environment.  Here we present lessons learned from these on-going initiatives to promote IWRM, with a focus on the role of freshwater science and conservation.