Various quantities of fertilizers and other soil amendments are applied to agricultural soils over time. This can lead to the gradual accumulation of several elements, which can represent a threat for soil quality and for soil functions. We developed a regional modelling tool for assessing element fluxes in agricultural soils and their temporal and spatial patterns. The tool uses georeferenced farm census data, remote sensing images, fertilization guidelines and other data sources. The model provides spatially explicit balances of Nitrogen, Phosphorus, Copper and Zinc. Thus, critical areas with increased risk of element accumulation can be identified. Moreover, the model allows the analysis of simple scenarios, related to economic or policy drivers. Therefore, one of the strengths of the model is the capability of assessing measures towards sustainable agricultural land use through scenario analysis.