<p>Tengchong County, Southwestern China, is a renowned volcanic region with abundant geothermal resources. This study systematically investigates the geochemical characteristics of hydrothermal waters in Tengchong, utilizing major and trace elements as well as hydrogen and oxygen isotopes. The primary objectives are to identify the potential sources of the hydrothermal waters and provide a detailed assessment of heavy metal pollution, with a particular focus on fluoride. The results of δD and δ¹⁸O values indicate that the hydrothermal waters primarily originate from atmospheric precipitation, with some samples (Dagunguo and Huangguajing) showing evidence of high-temperature water–rock interactions. The study reveals significantly high concentrations of F, Hg, and As in the geothermal waters, accompanied by heightened concentrations of other trace elements, including V, Cr, Cu, Zn, Cd, Sb, and Pb. Among these, F and Hg stand out as posing severe contamination risks, particularly at the Rehai and Xiangda sites where the highest water quality index (WQI) values were documented. The fluoride levels, in particular, far surpass safe drinking water thresholds, raising serious public health concerns. The study identifies key mechanisms for fluoride enrichment, including water–rock interactions, cation exchange, and high temperatures. Specifically, the dissolution of fluoride-bearing minerals like fluorite (CaF₂), enhanced by elevated temperatures, significantly contributes to fluoride release. Additionally, the exchange of calcium (Ca²⁺) with sodium (Na⁺) promotes fluoride enrichment in the geothermal waters. The study highlights the need for effective monitoring and management of geothermal resources to mitigate the risks associated with trace element contamination.</p>