The predicting groundwater nitrate pollution risk, especially in terms of changes in fertilizing, has not been fully investigated so far. In particular, there is no comprehensive method to assess this risk in areas of different land use type, and not only in agricultural areas. The aim of this study was to develop a novel multicriteria methodology for groundwater nitrate pollution risk assessment, which meets these issues. A further aim was to determine how much this risk would change if the amount of organic and synthetic fertilization was reduced. An assumption was that groundwater pollution risk is a combination of the potential adverse impacts of land use, fertilization, and intrinsic groundwater vulnerability to pollution. The impact of fertilization was holistically evaluated by balancing nitrogen from spatially differentiated the size of the breeding, species of livestock, manure and synthetic fertilizers input, and spatially differentiated topsoil, with nitrogen uptake by different crops. The nitrate concentration in the leachate was used as a measure of the impact of fertilization. This concentration was compared to the natural baseline nitrate concentration in groundwater. Three fertilization scenarios for groundwater pollution risk assessment in two study areas were discussed. Under typical agricultural, climatic, soil, and geological conditions in Europe for the current total fertilization level of 95-120 kg N ha−1 groundwater nitrate pollution risk is low and moderate, but for fertilization of 150-180 kg N ha−1, a reduction in the total fertilization (synthetic and manure) by 40 to 50% may be required to achieve low risk of degradation of natural groundwater quality. Predictive simulations of groundwater nitrate pollution risk confirmed that reducing synthetic and organic fertilization has an effect, especially in areas with intensive fertilization. This method may allow for a holistic and scenario-based assessment of groundwater pollution risk and may help decision-makers introduce solutions to manage this risk under conditions of climate change, preservation of groundwater quality, and food security.