The Nitrate Directive has only been implemented satisfactorily in a few EU countries. The Commission have accepted the Danish implementation of the directive based on the Plan for the Aquatic Environment II. The costs of this plan has been calculated to 70 million € or 2,0 € per kg N in reduced leaching. The farmers have paid 60% of the costs. The paper then describes an example of a regional analysis covering the River Basin of Ringkøbing Fjord in Denmark, which indicates the type of calculations needed to find the measures and costs in order to comply with parts of the Water Framework Directive (WFD). The analysis shows that the geographical position of the measures are very important in order to achieve the expected nutrient reduction. The current income varies a lot in the River basin and this might influence the choice of cost effective measures to reduce nutrient load. Furthermore a close link between environmental and economic modelling is required to insure the expected improvements for the environment at the expected costs. The paper concludes that finding the most cost efficient combinations of measures to achieve the complex goals for streams, lakes, fjords and groundwater represents a large challenge for researchers and policy makers.