In this paper we discuss the use of mineral pigments recovered in stratigraphic position from three excavated archaeological sites (Traful Lake area, Argentina) with the aim of providing information on selection and frequency of use of these raw materials. In this region, human occupation has been recorded since 4000 BP. In order to identify the chromophoric minerals, we applied wavelength dispersive X-ray fluorescence spectrometry, Raman spectroscopy, and X-ray diffraction techniques. Green, red, yellow ochre, and white pigments dated between 3490 and 590 BP were analyzed. The results show that different analytical techniques provide complementary information in order to identify the pigments. Green, red, and yellow samples are related to iron-based compounds. The green pigments can be associated with celadonite and the others with hematite. White samples revealed the presence of hydroxyapatite. Black dots, identified as carbon, were observed in several samples. Red pigments are always predominant, and their relative abundance increases in recent strata. Results are discussed in light of the context and previous reports of chroniclers.