In this paper, we discuss baseline geochemical maps of elements harmful to human health compiled using concentration data of 982 volcanic soil samples from the metropolitan and provincial areas of Napoli (1171 km2). Each sample was digested in aqua regia and analysed by ICP-MS and ICP-ES. For the compilation of baseline geochemical maps, we apply a recently developed multifractal IDW interpolation method and spectral analysis (S-A) using a new geochemistry-dedicated GIS (GeoDAS). The geochemical baseline in an area of heavy anthropogenic impact, such as the Neapolitan territory, includes the geogenic natural content (background) and the anthropogenic contribution in the soils. The definition and distinction of background (geogenic) values, as opposed to baseline values, are very important in environmental studies because legislation typically fixes the intervention limits for both organic and inorganic substances in soils as a function of local background values. Maps obtained by the S-A method show high baseline values for some metallic elements (Pb, Zn, Sb, Hg, Cd, Cr, Cu) which denote a clear anthropogenic contribution, due to the long period of constant human activities in the study area. These maps also show a high geogenic contribution most probably derived from hydrothermal fluids because the study area is located between two active volcanic fields (Mt. Somma–Vesuvius and Campi Flegrei), where geothermal fluids have been used for spas since Roman times. The maps obtained using the S-A method, implemented in GeoDAS, reflect both the geogenic and anthropogenic contribution, so they must be considered as baseline maps. In order to obtain background values, to be used as reference values for the environmental Italian Law 471/1999, we have applied the concentration–area fractal method (C-A) to classify the pixel values of baseline maps. R-mode factor analysis helped in interpreting data controlled by anthropogenic sources as opposed to those controlled by geogenic sources.