The Bajos Submeridionales (BBSS) (Argentina) is a 54,800 km2 hydrological system located at the distal part of the Salado-Juramento Fluvial Megafan (SJRM). Its climate evolves from humid-subtropical in the east to semiarid in the west. Its hydrogeological system is typical of extensive plains, topography locally imposes vertical flows and neotectonic elements define system boundaries and drains. These characteristics and poor data availability represent a major challenge for identifying a hierarchical subsurface flow system and the influence of neotectonics. This work characterizes the hydrogeology of the BBSS and proposes a conceptual model based on integrated systematic information including 453 water level, 145 hydrochemical, and 99 δ18O- δD data. Four hydrogeological units are identified (HU1–HU4), two of which are divided into sub-units based on their sedimentary sequence. The main chemical types are Na-Cl, Na-Cl/SO4, Na-HCO3/Cl, Na-Cl/HCO3, and HCO3-Na. Dominant ions are Na, Cl, and SO4. Measured electrical conductivity reaches values as high as 132,000 μS/cm. Water chemistry modifying processes include halite, gypsum, and carbonate dissolution; ion exchange; inter-HU water mixing; and evapo-concentration. δ18O-δD and EC-δ18O suggest the existence of subsurface flow sectors. In the south, shallow and medium depth groundwater flows respond to the current circulation of the SJRM. Recharge occurs in the sub-Andean Ranges and point discharges, at the western lakes and some lakes of the Golondrina-Calchaquí system. Precipitation recharges shallow flows locally in the north, center, and east. Extreme west HU2 and HU1 receive deep upward thermal flows through structural lineaments. Thus, the Otumpa Hills morpho-structure would be a barrier to shallow HU1 flow, though not to deep regional HU2 and HU4 flows. Regional groundwater flow is from NW to SE and both local and regional flows would discharge in the Paraná River. The new conceptual model developed helps to further understand the groundwater system of a large plain in South America.