Vital for human consumption, water is a scarce resource, particularly in the arid environments of Patagonia. In this study we analysed local perspectives and the use of different water sources, based on two case studies in rural communities of Mapuche and Creole ancestry inhabiting extra-Andean Patagonia in Chubut, Argentina. Water quality was evaluated using an ethnolimnological, interdisciplinary approach, taking into account local perspectives and scientific contributions. In addition, we analysed appropriation strategies, management and local organoleptic characteristics. The work was based on semi-structured interviews, tours guided by informants, and physicochemical and microbiological analysis of water sources. It was found that 92% of local inhabitants mainly used superficial and subterranean sources of water for consumption, among which stood out: river, streams, springs, wells, and boreholes. Differences were observed between local and scientific perspectives in terms of water quality (chemical and microbiological). Most water sources used by inhabitants presented water of deficient quality for human consumption (61%), whereas locals considered the water to be fresh, delicious, and transparent. Nevertheless, some points of agreement were found in terms of organoleptic characteristics (e.g., odour, colour) and physicochemical parameters in certain water sources. In general, locals do not recognise the deterioration of their water supply, but the importance of organoleptic characteristics in local perception should be highlighted. These aspects speak of a need to promote opportunities for dialogue, and implement effective health measures, taking local perspectives into account. Display omitted •Patagonian rural communities largely depend on surface and subterranean water.•Most water sources are not suitable for human consumption.•Organoleptic attributes play an important role in the perception of water quality.•Poor-quality water is not perceived locally as a health risk.•Local and scientific perspectives differ with respect to water quality.