Under the scope of a R&D Project for the use of GSHP systems in a Military facility near Lisbon, groundwater samples were collected for chemical and isotopic characterization since these shallow aquifers could represent the basis for this Project viability (i.e. the source of heat transfer – using groundwater from local dug wells). An isotopic difference around 1‰ in 18O and around 10 ‰ in 2H and deuterium excess d = 10 ‰, was found in the shallow groundwater samples, collected in an area of about 3 km2, where the pH values range from 7 to 10. The differences in the isotopic and chemical signatures could be ascribed to different recharge altitudes and/or different flow paths in the Lisbon Volcanic Complex, and to the existence of organic layers or linked to residues from old anthropogenic activities (δ13C measured in the total dissolved carbon vary from -23.5 to -14 ‰).