Short-wave infrared reflectance (SWIR) spectra obtained from a Portable Infrared Mineral Analyser (PIMA) were applied to map acidic mine soils at San Miguel massive sulphide deposit, Iberian Pyrite Belt, Spain. Field spectral measurements and laboratory analysis were performed on samples from 58 stations from two very polluted grounds. These analyses identified secondary and tertiary Fe-rich sulphate–hydrate minerals associated with the alteration of sulphide-bearing mine wastes and other associated infrared active minerals. The spectral absorption features for the pure salt types found in these areas allowed the preparation of a specific reference library for automatic mineral identification. Using this approach three separate zones around the sources of contamination have been discriminated: a “proximal” zone dominated by rozenite + hexahydrite, a “transitional” zone dominated by copiapite + coquimbite and a “distal” zone of hydronium–jarosite. An additional zone of “gypsum” was also recognized locally at the areas, where, last decade the neutralization of the acid soils with limestones was attempted. In addition to discriminating distinct mineralogical zones quantitative spectral data allowed contoured mineral maps to be produced that are comparable with the estimated mineralogical data obtained from conventional methods, such as XRD and field observations. These maps demonstrate that sulphate minerals were firstly formed by oxidation of the pyrite-rich ores followed by dissolution and precipitation involving a combination of oxidation, dehydration, and neutralization reactions. The study shows the potential of SWIR spectral analysis to identify and understand the distribution of efflorescent salts and other products of pyrite decomposition and provides a methodology to assist the research and monitoring of sources of environmental contamination.