Groundwaters circulating in Upper Mesozoic carbonates are of great interest for geothermal heat production and storage applications in the Geneva area. This study aims at providing new insights and proposing new interpretations about the mineral-water reactions and the fluid-flow paths mechanisms across the Geneva Basin (GB). Data from previous studies are combined and improved by new ones collected from cold and hot springs and geothermal exploration wells in 2018 and 2020 in the framework of the GEothermies program and HEATSTORE project. Major ions, trace elements, and the isotopes of Oxygen, Hydrogen, Sulfur, Strontium, and Carbo have been analysed and the results show that the sampled waters have a meteoric origin, the carbonate aquifers act as preferential host rocks for geothermal waters, and partial contribution from the Cenozoic sediments can be observed in some samples. The Jura Mountains and the Saleve Ridge are the main catchment areas and an evolution from a pure Ca-HCO3 footprint for the cold springs, to a Na > Ca-HCO3 and a Na-Cl composutions, is observed at the two geothermal wells. The residence time is in the order of a few years for the cold springs and reaches up to 15–20,000 years for the deep wells.