This article introduces a new web-based and freely accessible tool, the Nitrate Fate tool (NFt), for the assessment of groundwater vulnerability to nitrate pollution in a variety of pedoclimatic conditions. The contamination of water resources by nitrate, in fact, represents a growing and persistent global environmental problem, and the utilization of practical tools to assist personnel working in the agricultural sector is key for mitigating the impact on land use, while maintaining farmers’ incomes. The (NFt) has been developed and integrated into the geospatial decision support system, LandSupport, as a way to support multiple stakeholders in conducting the so-called what-if scenario analysis (e.g., what would happen to the crop production if I substitute a quote of inorganic fertilizer with the same quote of an organic one?). The tool couples a state-of-art crop-growth model—which simulates crop growth dynamics, the nitrogen and carbon cycles—with a novel transfer function model in order to assess the transport of nitrate through the unsaturated zone to the groundwater table. Within the LandSupport platform, the results are shown both as coloured maps and as cumulative charts representing the travel times and the concentrations of root leachate to groundwater table depths. This work details the tool’s rationale, the coupling of the models, and their implementation. Moreover, this article shows examples of applications supporting several public authorities and end-users, underlining that, by combining all of the information on soils, groundwater table depths, management and climates, it is possible to obtain a comprehensive understanding of nitrogen transport dynamics. Two case studies are presented: the Piana del Sele and the eastern plain of Naples, both located in the Campania region of Italy. The results of the tool’s applications reveal significant groundwater vulnerability in both plains, mainly due to the shallow groundwater table depths, resulting in remarkably fast mean nitrate travel times ranging from 0 to 6 years. Finally, the tool provides a reproducible and replicable solution, and future implementation is foreseen for additional case studies all over the world.