A strong normative development in Europe, including the Nitrate Directive (1991) and the Water Framework Directive (WFD) (2000), has been promulgated. The WFD states that all water bodies have to reach a good quantitative and chemical status by 2015. It is necessary to consider different objectives, often in conflict, for tackling a suitable assessment of the impacts generated by water policies aimed to reduce nitrate pollution in groundwater. For that, an annual lumped probabilistic model based on Bayesian networks (BNs) has been designed for hydro-economic modelling of groundwater quality control under uncertain conditions. The information introduced in the BN model comes from different sources such as previous groundwater flow and mass transport simulations, hydro-economic models, stakeholders and expert opinion, etc. The methodology was applied to the El Salobral–Los Llanos aquifer unit within the ‘Easter Mancha’ groundwater body, which is one of the largest aquifers in Spain (7,400 km2), included in the Júcar River Basin. Over the past 30 years, socioeconomic development within the region has been mainly depending on intensive use of groundwater resources for irrigating crops. This has provoked a continuous groundwater level fall in the last two decades and significant streamflow depletion in the connected Júcar River. This BN model has proved to be a robust Decision Support System for helping water managers in the decision making process.