Water quality is a major problem nowadays around the world. CLEANWATER system combine various information and complex data in order to evaluate the present level of nutrient pollution in vulnerable areas, as well as to assess the cost-efficiency of the measures that could be applied. Through a simple and intuitive web interface, CLEANWATER offers the decision makers a spatial aware tool to (1) create scenarios related to the human activities and climate changes, (2) send those scenarios to numerical models to model future evolution of water quality and (3) view, query and perform spatial analysis of the simulation results. The system was implemented in a test river basin (Barlad River Basin in Eastern part of Romanian) and started to contribute to the development of a modern water management system, according to EU legislation (e.g. Water Framework Directive, Nitrates Directive). The future plan is to replicate the system at national and international level. The system is build entirely with standard compliant free and open source software applications like OpenLayers, ExtJS, PostGIS, GeoServer and GDAL.