In recent years, the significant improvement in point source depuration technologies has highlighted problems regarding, in particular, phosphorus and nitrogen pollution of surface and groundwater caused by agricultural non-point (diffuse) sources (NPS). Therefore, there is an urgent need to determine the relationship between agriculture and chemical and ecological water quality. This is a worldwide problem, but it is particularly relevant in countries, such as Hungary, that have recently become members of the European Community. The Italian Foreign Ministry has financed the PECO (Eastern Europe Countries Project) projects, amongst which is the project that led to the present paper, aimed at agricultural sustainability in Hungary, from the point of view of NPS. Specifically, the aim of the present work has been to study nitrates in Hungary's main aquifer. This study compares a model showing aquifer intrinsic vulnerability to pollution (using the DRASTIC parameter method; Aller et al. [Aller, L., Truman, B., Leher, J.H., Petty, R.J., 1986. DRASTIC: A Standardized System for Evaluating Ground Water Pollution Potential Using Hydrogeologic Settings. US NTIS, Springfield, VA.]) with a field-scale model (GLEAMS; Knisel [Knisel, W.G. (Ed.), 1993. GLEAMS—Groudwater Leaching Effects of Agricultural Management Systems, Version 3.10. University of Georgia, Coastal Plain Experimental Station, Tifton, GA.]) developed to evaluate the effects of agricultural management systems within and through the plant root zone. Specifically, GLEAMS calculates nitrate nitrogen lost by runoff, sediment and leachate. Groundwater monitoring probes were constructed for the project to measure: (i) nitrate content in monitored wells; (ii) tritium ( 3H) hydrogen radioisotope, as a tool to estimate the recharge conditions of the shallow groundwater; (iii) nitrogen isotope ratio δ 15N, since nitrogen of organic and inorganic origin can easily be distinguished. The results obtained are satisfactory, above all regarding the DRASTIC evaluation method, which is shown to satisfactorily explain both low and high aquifer vulnerability, and furthermore proves to be a good tool for zoning hydrogeological regions in terms of natural system susceptibility to pollution. The GLEAMS model, however, proves not to be immediately usable for predictions, above all due to the difficulty in finding sufficient data for the input parameters. It remains a good tool, but only after an accurate validation, for decision support systems, in the specific case to integrate intrinsic vulnerability, from DRASTIC (or similar methods), with land use nitrate loads from GLEAMS, or similar methods. The PECO project has proved a positive experience to highlight the fundamental points of a decision support system, aimed to mitigate the nitrate risk for groundwater coming from Hungarian agricultural areas.