In Europe, 30% of groundwater bodies are considered to be at risk of not achieving the Water Framework Directive (WFD) 'good status' objective by 2015, and 45% are in doubt of doing so. Diffuse agricultural pollution is one of the main pressures affecting groundwater bodies. To tackle this problem, the WFD requires Member States to design and implement cost-effective programs of measures to achieve the 'good status' objective by 2027 at the latest. Hitherto, action plans have mainly consisted of promoting the adoption of Agri-Environmental Schemes (AES). This raises a number of questions concerning the effectiveness of such schemes for improving groundwater status, and the economic implications of their implementation. We propose a hydro-economic model that combines a hydrogeological model to simulate groundwater quality evolution with agronomic and economic components to assess the expected costs, effectiveness, and benefits of AES implementation. This hydro-economic model can be used to identify cost-effective AES combinations at groundwater-body scale and to show the benefits to be expected from the resulting improvement in groundwater quality. The model is applied here to a rural area encompassing the Hesbaye aquifer, a large chalk aquifer which supplies about 230,000 inhabitants in the city of Liege (Belgium) and is severely contaminated by agricultural nitrates. We show that the time frame within which improvements in the Hesbaye groundwater quality can be expected may be much longer than that required by the WFD. Current WFD programs based on AES may be inappropriate for achieving the 'good status' objective in the most productive agricultural areas, in particular because these schemes are insufficiently attractive. Achieving 'good status' by 2027 would demand a substantial change in the design of AES, involving costs that may not be offset by benefits in the case of chalk aquifers with long renewal times.