This contribution constitutes a revision of the stratigraphic and hydrogeologic framework of the Magallanes aquifer system based on previous work, well logs correlations, outcrop observations and new geochronologic data. The system can generally be divided into three hydrostratigraphic units separated by significant unconformities, from base to top: El Salto-Filaret, Palomares and Cabo Negro. The El Salto and Filaret formations are considered latest Oligocene to early Miocene in age, and they may contain both infiltrated and connate seawater. The Palomares Formation is early to middle Miocene in age, and the Cabo Negro formation, composed of glacial and glaciofluvial sediments, represents the Holocene cover in the region. Groundwater chemistry from wells indicates potable water only in Palomares and Cabo Negro, especially in the latter. Depending on the sedimentary configuration, aquifers may vary from confined in the bedrock to free in the Quaternary cover, but in the latter confined and semiconfined may also occur. Aquifers below the mean sea level and close to the Magallanes Strait locally contains brackish water suggesting lateral encroachment of saltwater from coastal areas. Better knowledge of groundwater characteristics and implementation of key policies to identify and mitigate potential groundwater mismanagement and/or contamination is necessary for sustainable exploitation of natural resources, aquifers’ protection, and the social understanding of their safe development.