A variety of organic compounds in the thermal waters of the Central Baikal Rift Zone were studied. The research was based on solid-phase extraction method that was carried out in-situ. We considered N2-thermal waters of SO4-Natype and N2-CH4 thermal waters of HCO3-SO4-Na type with temperatures at the surface ranging between 19.875.6 °C. We identified 211 organic components with molecular weights from 92 to 506 daltons using gas chromatography-mass spectrometry. The dissolved organic carbon concentration was on average 0.7 mg/L. DOC origin is autochthonous with a small contribution from plant detritus. It was established that normal and iso-alkanes, aromatic hydrocarbons and ethers are dominant organic compounds in the thermal springs. The origin of these compounds is predominantly bacterial with the contribution of thermocatalytic processes in the formation of some linear alkanes and aromatic hydrocarbons. In addition, we found correlation between the main homologous series of organic matter, major ions and physicochemical parameters. These correlations showed a decrease of ethers and phthalates concentrations and an increase of heteroaromatic hydrocarbons and terpenes content due to an increase of fluorine ion. Moreover, the terpenes accumulation impacts DOC which concentration increases too. In turn, aliphatic hydrocarbons initiate the formation of aromatic ones, entering reactions of cycloaddition, polymerization, dehydrocyclization, etc. In addition, some compounds indicate an insignificant technogenic pollution of the studied thermal springs in the Central Baikal Rift Zone.