In the XIX th century, the Alfama thermal and non-thermal springs were qualified as “mineral water” by the governmental authorities. But after a few years of legal usage in balneotherapy, all of them knew a constant and progressive definitive decay, and the last balneotherapic facility was abandoned and sealed more than 40 years ago. Despite their significant influence in Lisbon life along the History, their exact location is now only approximate. Nowadays, they are all buried below the city buildings, squares and streets. Since some of the Alfama springs reached temperatures up to 34 °C, groundwater from these springs can be used in a new modern spa or in district heating facilities in the heart of the city of Lisbon, if adequately recovered. But priorly, to carry out this task, a global understanding of the conceptual hydrogeological model is needed. However, the springs are located in a densely urbanized and touristic area, where geological outcrops are no longer visible and old springs’ location is unknown; therefore, a review of geological and hydrogeological data and geotechnical reports was carried out to plan further research works. Adding to this exhaustive bibliographic review and data integration, new seismic reflection data were acquired, and brought some new insights on the groundwater circulation system. All these data interpretations contributed significantly to achieve a better knowledge on the main and secondary faults that control the occurrence of Alfama springs and framed them into the complex regional tectonic framework. The entire set of historical hydrogeological data, geotechnical information, and newly acquired data lead to a reasonably accurate and data supported 3D geological and hydrogeological conceptual model of the deep groundwater flow circuit. This paper describes the research work that led to the conception of the local and complex 3D hydrogeological model of the Alfama springs system. With this 3D model, the best location for a dipped well can now be envisaged, keeping in mind the narrow local urban constraints, possible future users, and stakeholders.