Water scarcity has been a feature of life in the Jordan River basin from time immemorial. Over the last century the situation has become gradually worse because of the increasing population, its development for agriculture and changes in rainfall patterns and consequent droughts. The potential impact of global change on the region is likely to be very damaging unless steps are taken to adapt. The roughly forty interdisciplinary research teams taking part in the GLOWA Jordan River Project, whose membership is made up of scientists and stakeholders from Germany, Israel, Jordan and Palestine, produced numerous results of applied and basic research about the effects of global change and alternative options for responding to them. The results included regional climate change scenarios, scenarios for regional development under global change, improved understanding of the hydrological conditions in the region, and water management application tools such as the Water Evaluation and Planning (WEAP) tool. The project developed strategies and guidelines for sustainable water and land management under global change. It integrated among many different disciplines like climatology, hydrology, ecology, socio-economy, and agriculture and supported an active transboundary dialogue between science and stakeholders in the Jordan River region. A transdisciplinary approach was realized by developing jointly with stakeholders scenarios of the water situation and potential adaptation strategies via a scenario analysis approach, as well as by developing and establishing WEAP usage with regional stakeholders. The project can serve as an example for successful transboundary IWRM even in the most contentious setting.