The water quality management tool RIONET for river basins has been developed with regard to the EU Water Framework Directive. The management tool can simulate the water quality in catchment basins not only in the dimension of a single river but in whole river networks. A submodel of the IWA River Water Quality Model No. 1 is used in RIONET. The river model is based on the assumption that self purification processes in the river takes place both in the benthic biofilm and the bulk water phase. Laboratory experiments with sediment cores underline the major role of the benthic biofilm. The input parameters of the management tool such as volumetric flow rates from waste water treatment plants and flow velocities and discharge in the main river and its tributaries can be loaded directly from geographic information systems (GIS). The subcatchment basin of the river Bode in Saxon Anhalt was used for test runs of RIONET.