Research and development in hydroinfomatics can play an important role in environmental impact assessment by integrating physically-based models, data-driven models and other Information and Communication Tools (ICT). An illustration is given in this paper describing the developments around the Soil and Water Assessment Tool (SWAT) to support the implementation of the EU Water Framework Directive. SWAT operates on the river basin scale and includes processes for the assessment of complex diffuse pollution; it is open-source software, which allows for site-specific modifications to the source and easy linkage to other hydroinformatics tools. A crucial step in the world-wide applicability of SWAT was the integration of the model into a GIS environment, allowing for a quick model set-up using digital information on terrain elevation, land use and management, soil properties and weather conditions. Model analysis tools can be integrated with SWAT to assist in the tedious tasks of model calibration, parameter optimisation, sensitivity and uncertainty analysis and allows better understanding of the model before addressing scientific and societal questions. Finally, further linkage of SWAT to ecological assessment tools, Land Use prediction tools and tools for Optimal Experimental Design shows that SWAT can play an important role in multi-disciplinary eco-environmental impact assessment studies.