Thermal groundwater in the Lower and Middle Triassic carbonates in Chongqing, China, is mainly concentrated in anticlines. Hot springs (32.9 to 57 °C) with SO4-Ca type waters and Total Dissolved Solids (TDS) of 1620 to 2929 mg/L emerge in the middle and the plunging ends of the structures. Multivariate methods are used to analyze the hydrochemical characteristics of the waters, and identify the sources of the main dissolved components, providing an insight into the evolution of the environment in which they formed. Hierarchical cluster analysis of compositional data differentiates samples in the study area into three categories: high TDS-high Ca2+ and SO42− water; medium TDS-high Na+ and Cl− water; and low TDS-high HCO3− water. Factor analysis and ion ratio relationships show that Ca2+ and SO42− are mainly derived from the dissolution of gypsum and anhydrite within the geothermal reservoir, with some addition of SO42− from coal-bearing cap rocks. The main source of HCO3−, is in the dissolution of dolomite and CO2 that also promotes the incongruent dissolution of albite and K-feldspar, adding Na+ and K+ to the groundwater. Reverse modelling of the transfers of each phase shows, in three models, that the minerals dissolved decrease progressively—with the exception of halite and albite. Combined with the hydrochemical characteristics of hot water in the same reservoir in the adjacent area (Cl-Na type, TDS of 13.37 g/L), a process of desalination of the hot water can be confirmed, which has not yet reached the ‘freshwater’ stage dominated by HCO3−.