The isotopic ratios of H, O and C in water within the Long Valley caldera, California reflect input from sources external to the hydrothermal reservoir. A decrease in δD in precipitation of 0.5‰ km⁻¹, from west to east across Long Valley, is caused by the introduction of less fractionated marine moisture through a low elevation embayment in the Sierra Nevada Mountain Range. Relative to seasonal fluctuations in precipitation (−158 to −35‰.), δD ranges in hot and cold surface and groundwaters are much less variable (−135 to −105‰.). Only winter and spring moisture, reflecting higher precipitation rates with lighter isotopic signatures, recharge the hydrological system. The hydrothermal fluids are mixtures of isotopically heavy recharge (δD = − 115‰, δ¹⁸O = − 15‰) derived from the Mammoth embayment, and isotopically lighter cold water (δD = −135‰, δ¹⁸O = −18‰). This cold water is not representative of current local recharge. The δ¹³C values for dissolved carbon in hot water are significantly heavier (− 7 to − 3‰) than in cold water (−18 to −10‰) denoting a separate hydrothermal origin. These δ¹³C values overlie the range generally attributed to magmatic degassing of CO₂. However, δ¹³C values of metamorphosed Paleozoic basement carbonates surrounding Long Valley fall in a similar range, indicating that hydrothermal decarbonization reactions are a probable source of CO₂. The δ¹³C and δ¹⁸O values of secondary travertime and vein calcite indicate respective fractionation with CO₂ and H₂O at temperatures approximating current hydrothermal conditions.