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The thermal mineral water of Peñón de los Baños spa (Mexico City) has been used for over 500 years starting in pre-Hispanic times and is famous for the treatment of various pathologies. It has a temperature of 45 °C, which is rich in HCO 3 - , and its main trace elements are B, Li and Fe, which confers healing effects. Concerns about the sustainability of this important spa have motivated this study to understand the thermal system, possible hydraulic and hydrochemical changes over time and its implications. Stable water isotope data indicate that the thermal water sources originate from local precipitation at Sierra de las Cruces with a recharge elevation of approximately 2770 m above sea level. The recharged water percolates through volcanic and carbonate rock formations and ascends via fault structure conduits, where it eventually is extracted 25 km downstream in Peñon de los Baños. During the gravity-driven deep circulation of up to 4.9 km, the groundwater is heated up to 136-160 °C. A comparison of past and current water levels and water chemical analyses indicates a water table drop and few variations in the chemical composition, confirming the presence of anthropic impact on water quality. Due to the heavy groundwater extractions in Mexico City, the spring water flow has ceased, and water must be pumped now from a 203-m deep well. In addition, the concentration of bicarbonate, sodium and chloride has been reduced by half since the onset of groundwater development. The therapeutic effects of this thermal mineral water are at risk due to the alteration of the chemical signature. However, new and different therapeutical uses may prevent a future deterioration or closure of this historically important thermal spa. It is crucial to establish a monitoring program of the thermal mineral water and reducing or minimizing nearby urban extractions which tap the regional flow component to preserve the properties of the thermal water., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)