Shallow, low-temperature geothermal resources can significantly reduce the environmental impact of heating and cooling. Based on a replicable standard workflow for three-dimensional (3D) geothermal modeling, an approach to the assessment of geothermal energy potential is proposed and applied to the young sedimentary basin of Pisa (north Tuscany, Italy), starting from the development of a geothermal geodatabase, with collated geological, stratigraphic, hydrogeological, geophysical and thermal data. The contents of the spatial database are integrated and processed using software for geological and geothermal modeling. The models are calibrated using borehole data. Model outputs are visualized as three-dimensional reconstructions of the subsoil units, their volumes and depths, the hydrogeological framework, and the distribution of subsoil temperatures and geothermal properties. The resulting deep knowledge of subsoil geology would facilitate the deployment of geothermal heat pump technology, site selection for well doublets (for open-loop systems), or vertical heat exchangers (for closed-loop systems). The reconstructed geological-hydrogeological models and the geothermal numerical simulations performed help to define the limits of sustainable utilization of an area's geothermal potential.