In the context of global climate change, understanding the relationships between climate and groundwater is increasingly important. This study in the NW Alps represents the first regional-scale investigation of the groundwater feature variation in mountain aquifers due to climate variability. The analysis of groundwater temperature and discharge in 28 natural mineral water springs and meteorological parameters (rainfall and air temperature) permitted us to evaluate the annual behaviour and possible trends of these parameters during the period from 2001 to 2018. The air temperature showed a positive trend almost everywhere, with a rise of up to 0.03 °C/year. In contrast, only ten springs showed a positive trend for groundwater temperature, but with the smallest rates of increase. Moreover, despite the substantial stability of the rainfall amount, 50% of the analysed springs showed a trend (29 and 21% for positive and negative trends, respectively) with low discharge variations. Finally, cross-correlation analyses proved the close relationship between air and groundwater temperatures, with a time lag between 0 and 3 months, and between spring discharge and air temperature, with a time lag between 1 and 3 months. In particular, spring discharge is closely connected to snow melting in spring and subordinate to rainfall. These results highlight the existing correlations between spring discharge and various meteorological and topographic parameters in the studied mountain area and provide a preliminary framework of the impacts of climatic variability on the availability and temperature of the exploited water resources.