Near-surface geophysical techniques are useful for the characterization of archaeological areas because of their ability to rapidly cover wide extensions and obtain high-resolution data to identify the location for archaeological excavations. However, in hyperarid environments usual geophysical techniques may fail to obtain the expected results due to the dry near surface. This study proposes an integration of ground penetrating radar (GPR) and electromagnetic induction (EMI) techniques, to elucidate the origin of thousands of aligned circular features located at the Iluga archaeological area emplaced on one of the driest places on Earth (Pampa del Tamarugal, Atacama Desert). The GPR was useful to recognize alluvial deposits, sandy aeolian filling in pre-existing holes and roots right underneath circular features. Magnetic susceptibility data derived from the EMI in-phase component, usually considered a complementary result, were useful to identify fireplaces in the vicinity of the alignments. These geophysical findings were verified with an archaeological excavation. It has been found that circular features resulted from an extensive deforestation process in the Pampa del Tamarugal, consisting in the extraction of both trunk and roots of algarrobos (Prosopis chilensis) or tamarugos (Prosopis tamarugo), likely for recent charcoal production. The proposed methodology delivers promising results for archaeological and shallow geological studies in hyperarid and dry environments.