Water resources management can be challenging when confronted with pollution, water shortage, floods, water-related diseases, climate change and variability. In this thesis, it is assessed how the management of a multi-functional river basin can be facilitated through the development and testing of analytical tools in data-poor and data-rich context. A variety of tools and strategies is developed and tested on a variety of stakeholder selected themes, namely: •Cost-effective improvement of water quality in the Nete river (Belgium) •An early warning system for flash floods in hyper-arid Egypt •Integration of human health in wetland management in the Inner Niger Delta (Mali). This thesis arguments that the development of tools can support integration and cooperation between experts and decision-makers. If there is a perceived lack of data and capacity, besides questioning the tool complexity, equally important is the process used for model development and stakeholder involvement.