Agriculture is to a large part responsible for nitrate leaching into groundwater and rivers in Germany, especially in highly intensive agricultural regions. To evaluate the link between nitrogen surpluses from agriculture and nutrient leaching into ground- and surface waters, a model network to analyse current and future nitrogen surplus developments and water quality is set up by connecting hydrological and hydrogeological models with the German agricultural sector model RAUMIS. A set of different environmental measures and their costs is selected to fulfil surface and groundwater targets of the European water framework directive (WFD) for the case of the Weser River basin. Results show that with additional agri-environmental measures covering around 1 million hectares agriculturally used land with total costs of 100 million Euros the objectives of the WFD could be achieved until 2015. Sensitivity analysis allows a better valuation of the range of the costs. The costs and volumes are compared to regional farming characteristics and subsidies. Results show that costs of additional environmental measures would take up 5% of current direct payments to farmers. The work represents an interdisciplinary area wide modelling approach to evaluate agricultural input and measures together with an approach to quantify costs to achieve environmental objectives of the WFD.