The recent rapid increase in urbanization has led to the inclusion of underground spaces in urban planning policies. Among the main subsurface resources, a strong interaction between underground infrastructures and groundwater has emerged in many urban areas in the last few decades. Thus, listing the underground infrastructures is necessary to structure an urban conceptual model for groundwater management needs. Starting from a municipal cartography (Open Data), thus making the procedure replicable, a GIS methodology was proposed to gather all the underground infrastructures into an updatable 3D geodatabase (GDB) for the metropolitan city of Milan (Northern Italy). The underground volumes occupied by three categories of infrastructures were included in the GDB: (a) private car parks, (b) public car parks and (c) subway lines and stations. The application of the GDB allowed estimating the volumes lying below groundwater table in four periods, detected as groundwater minimums or maximums from the piezometric trend reconstructions. Due to groundwater rising or local hydrogeological conditions, the shallowest, non-waterproofed underground infrastructures were flooded in some periods considered. This was evaluated in a specific pilot area and qualitatively confirmed by local press and photographic documentation reviews. The methodology emerged as efficient for urban planning, particularly for urban conceptual models and groundwater management plans definition.