Nowadays, the promotion of interested stakeholder integration and participation in water resource planning and management plans is forcing to create and use more sophisticated and appropriate software tools, models and planning frameworks at regional scales. In this session we look at the identification of both the strengths and limitations of such tools, and the types of problems and issues each tool is able to analyze and that has been addressed in actual applications. We focus on some issues relevant to the gap between the claimed usefulness of tools in the academic literature and their demonstrated utility. Presenters will emphasize their experiences in customizing tools for improving modeling usability in practical solutions of water management and planning problems including related environmental and ecological aspects. Generally, the expected outcome of this session will be a comprehensive description of research needs and challenges in developing and applying improved tools for analyzing the increasingly complex water resources issues that system managers will face in the future.