The implementation schedule for the EU water framework directive requires the creation of monitoring programmes for water bodies according to the intensity of the pollution risk by the end of 2006. Until 2009 river basin district management programmes have to be established followed by the implementation of measures from the management plans (until 2012). The WAgriCo-project (Water Resources Management in Cooperation with Agriculture), is a collaborative project funded by the European Commission Life Fund within the period October 2005 to September 2008, involving six British and four German institutions. The WAgriCo-project is based around the catchment management process, of identifying diffuse pollution issues and potential management solutions, involving land managers/advisors to implement methods and to assess their effectiveness in terms of pollution reduction and costs. For a basic understanding of the interactions between these issues an integrated hydrological/hydrogeological conceptual model has been set up. The model consists of three main features: natural characteristic assessment, anthropogenic impact assessment using monitoring data and model tools providing a linkage between the first two parts. In this paper the application of the integrated hydrological/hydrogeological conceptual model for geographical prioritization and determination of environmental target areas in the case study area Grosse Aue in the Federal State of Lower Saxony, Germany is described and discussed. It is demonstrated how area differentiated parameters like the denitrification condition in soils, the runoff ratio, nitrate concentrations in the leachate and groundwater monitoring data are determined and combined in order to determine target areas. With the given example of the case study area Grosse Aue, the importance of defining the receptor of nitrate outputs (groundwater or surface water) and the environmental target prior to the delineation of environmental target areas could be shown.