We used the interdisciplinary model network AGRUM [corrected] to predict the actual mean nitrate concentration in percolation water at the scale of the Weser river basin (Germany) using an area differentiated (100 m x 100 m) approach. AGRUM [corrected] combines the agro-economic model RAUMIS for estimating nitrogen surpluses and the hydrological models GROWA/DENUZ for assessing the nitrate leaching from the soil. For areas showing predicted nitrate concentrations in percolation water above the European Union (EU) groundwater quality standard of 50 mg NO3-N/L, effective agri-environmental reduction measures need to be derived and implemented to improve groundwater and surface water quality by 2015. The effects of already implemented agricultural policy are quantified by a baseline scenario projecting the N-surpluses from agricultural sector to 2015. The AGRUM [corrected] model is used to estimate the effects of this scenario concerning groundwater and surface water pollution by nitrate. From the results of the model analysis the needs for additional measures can be derived in terms of required additional N-surplus reduction and in terms of regional prioritization of measures. Research work will therefore directly support the implementation of the Water Framework Directive of the European Union in the Weser basin.