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Water quality characterization and assessment are key to protecting human health and ecosystems, especially in arid areas such as northern Chile, where water resources are scarce and rich in pollutants. The objective of this study was to review and assess available official water quality data in the Chilean Altiplano-Puna basins for a 10-year period (2008–2018), including water treatment systems. Within the 43,600 km 2 of Chilean Altiplano-Puna territory, only 16 official water quality monitoring stations had up-to-date data, and the sampling frequency was less than 3 per year. Most of the water samples collected at the evaluated stations exceeded the drinking and irrigation water Chilean standards for arsenic, boron, and electrical conductivity. Moreover, the characteristics of the Altiplano-Puna affect water quality inside and beyond the area, limiting water usage throughout the Altiplano-Puna basins. Drinking water treatment plants exist in urban and rural settlements; however, the drinking water supply in rural locations is limited due to the lack of adequate treatment and continuity of service. Wastewater treatment plants operate in some urban locations but rarely exist in rural locations. Limited data impede the proper assessment of water quality and thus the evaluation of the need for treatment systems. As such, the implementation of public policies that prioritize water with appropriate quantity and quality for local communities and ecosystems is imperative. Supplementary Information The online version contains supplementary material available at 10.1007/s10661-022-10628-1.