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Most of the developed countries have several methods for delineating well and spring protection zones. However, the definition of protection zones on groundwater systems in fractured media in urban areas cannot be developed through a single approach due to the great diversity of geological and hydrological conditions, including urban and heritage constraints. Therefore, the best approach is to apply and cross-check several methods related to the intrinsic vulnerability of groundwater systems. The so-called DISCO method permits, at a local scale, a reliable evaluation of the vulnerability protection zones of springs in fissured media. Moreover, urban environments have unique characteristics that should be included in this assessment, namely land cover and hydraulic features. Therefore, an updated Geographic Information System (GIS)-based mapping methodology is proposed, termed DISCO-Urban. As a result, a multidisciplinary approach, organized and integrated on a GIS-based mapping, was developed to evaluate urban groundwater vulnerability to contamination combining climatology, geology, hydrogeology, hydrogeomorphology, hydrogeotechnics, urban hydraulics, and land use/cover. This study highlights the importance of urban hydrogeological mapping as a valuable tool to support urban hydrogeological conceptualisation and delineate protection zones on historical springs of the Arca D’Água site in the Porto urban area (NW Portugal). At over 600 years old, those ancient springs are extensive underground galleries and aqueducts man-made to supply the fountains systems in Porto city. Moreover, this approach embraces a hydrogeoethical framework of values shared by all agents involved to achieve a balanced and ethical design with nature, heritage and society.