The Water Framework Directive requires EU Member States to analyse economic impacts of the Directive's implementation. To reach a "good status", instruments have to be judged according to their cost-effectiveness. We evaluate costs and effects of measures to reduce nitrate emission of Austrian agriculture. Results are based on a model that integrates production decisions with stochastic environmental outcomes. The Directive's requirement to involve stakeholders may make it necessary to take a large number of indicators into consideration. We find that alternative calculations of the effectiveness criterion give different rankings of the most effective combination of measures.