The introduction of the Water Framework Directive in 2000 (European Parliament and Council 2000) has incentivised policy-makers to bring the quality of all water streams in EU member states up to a ‘good ecological status’ by 2015. Although a lot of work has been carried out since the introduction of the Directive, it is also evident that progress in improving water quality has been very slow. The main reason for such slow progress is the lack of robust evidence about the sources of pollution and the effects of possible mitigation measures. Also, there is insufficient knowledge regarding the economic implications of the various mitigation options. In this paper we introduce a microsimulation model that can help policymakers to evaluate the economic impact of Nitrogen (N) mitigation measures. In this initial case study, two measures are considered: 1) a stocking rate reduction to achieve a maximum level of organic nitrogen of 170 kg/ha; 2) a 20 percent stocking rate reduction. The results of this study confirm the hypothesis that introduction of these measures would lead to reduction in farm gross margins, which is consistent with the previous research in Ireland and UK.