Water scarcity and associated risks are serious societal problems. A major challenge for the future will be to ensure the short-term and long-term provision of accessible and safe freshwater to meet the needs of the rapidly growing human population and changes in land cover and land use, where conservation and protection play a key role. Through a Bayesian spatial statistical method, a time-dependent approach for groundwater vulnerability assessment is developed to account for both the recent status of groundwater contamination and its evolution, as required by the European Union (Groundwater Directive, 2006/118/EC). This approach combines natural and anthropogenic factors to identify areas with a critical combination of high levels and increasing trends of nitrate concentrations, together with a quantitative evaluation of how different future scenarios would impact the quality of groundwater resources in a given area. In particular, the proposed approach can determine potential impacts on groundwater resources if policies are maintained at the status quo or if new measures are implemented for safeguarding groundwater quality, as natural factors are changing under climatic or anthropogenic stresses.