The Salto–Arapey Aquifer System (SAAS) represents a complex hydrogeological framework composed of a detrital aquifer that lays over a fissured one in the Chaco-Paraná Basin. To enhance our understanding of this underground system, an initiative was undertaken to characterize a specific sector of the SAAS utilizing a geophysical methods known as Audiomagnetotelluric sounding. The primary outcomes of this endeavor include the geoelectrical characterizations of key formations and the development of a 2.5D geological-geophysical model. This endeavor significantly advances our geological and geophysical comprehension of the targeted sector, thereby offering substantial societal and economic benefits. Although the method did not allow differences between sedimentary formations, it did allow the recognition of altered basalts, which would facilitate the identification of areas with considerable potential for the productive development of water wells. Notably, this investigation holds significant local relevance as it presents a replicable methodology to characterize the rest of the system, or even aquifers sharing similar characteristics.