Soil is a very complex medium made of minerals, organic matter, microorganisms, air, and water. Vibrational spectroscopy techniques are exceptionally well-suited to be used with portable and hand-held devices. In this study, NIR spectroscopy was applied using portable instrumentation and the holistic Aquaphotomics approach to identify the differences in three Mediterranean soil profiles from Sardinia (Italy). The soil samples (95) collected from alluvial and loess-sampling sites in the three study areas of North Sardinia (i.e., Arborea, Berchidda, and Ottava) underwent preliminary oven-drying at 40 °C and sieving (mesh size of 2 mm) to remove skeletal particles, large roots, and organic debris. Data on soil spectra were collected in duplicate using the microNIR OnSite-W spectrometer (VIAVI Srl, Italy) in reflectance mode from 900 – 1,600 nm (50 scans; 125 reading points). Then, the data on the absorbance from 1,300 to 1,550 nm were statistically processed to construct the aquagrams and perform a PCA (95% confidence level). The suitability of using a portable instrument to identify the kind of soil in different areas, for example, in areas that have undergone desertification, can help in soil classification and the rapid and non-destructive analysis of its characteristics. The Aquaphotomics approach could detect considerable variation (particularly in the soil from Arborea) associated with the sampling depth.