—The paper presents new data on the composition of organic matter and the molecular-weight distribution of saturated hydrocarbons in the thermal waters of the Annenskoe field. The TIC chromatograms of extracts of the thermal waters, obtained by capillary gas chromatography–mass spectrometry, revealed 98 organic compounds of biogenic, thermogenic, and technogenic origin. The technogenic components amount to no more than 5%. The geochemical odd–even preference indices of saturated hydrocarbons (CPI, ACL, OEP, and TARHC) are calculated. It is shown that organic matter, in particular, saturated hydrocarbons, results from two processes: thermogenic processes in the water–rock system and bacterial activity. Variations in the composition of organic matter in the Annenskoe thermal waters have been determined for the first time. They are characterized by minor fluctuations within 30 min and serious fluctuations over two years and are expressed as an increase in the portion of thermogenic alkanes and a decrease in the portion of nitrogen-containing components.