Equilibrium in the H2O-H2-CO2-CO-CH4 gas system has been extensively applied to fumarole data for geothermal exploration and volcano monitoring. However, little is known about its application to two-phase (vapor and liquid) geothermal well fluids, which can show an excess of enthalpy. Here, we applied the H2O-H2-CO2-CO-CH4 gas indicators to two-phase geothermal well discharges from the Krafla geothermal system, Iceland, to estimate aquifer temperatures and identify secondary processes during resource exploitation. Results suggest that the Krafla resource is drawn from a deep (approximately between –500 and –1,600 m a.s.l.), two-phase aquifer with temperatures ranging from 272 to 320 °C and vapor fractions between 0.26 and 0.93, explaining the excess enthalpy observed in well fluids. These estimates align with the temperatures of the main production zones of geothermal wells, whereas solute geothermometers (SiO2 and Na/K) appear to record lower temperatures of minor, shallower, liquid aquifers. Wells with liquid-like enthalpy are sourced from the two-phase aquifer but are also influenced by water reinjection or downflows from a colder, shallower aquifer, consistent with the isothermal zone extending approximately between 400 and –900 m a.s.l. in Leirbotnar and Vesturhlíðar subfields. Water isotopes indicate the main aquifer is recharged by meteoric and reinjection fluids. Excess-enthalpy discharges show an influx of Ar- and N2-rich vapor, with depleted 40Ar/36Ar and δ15N values, suggesting fractionations of atmospheric gases dissolved into the reservoir liquid. On the other hand, δ13CCO2 and 3He/4He values point to a mantle origin, despite the lower δ13CCO2 and PCO2 levels that reflect a degassed magma (i.e., a noneruptive phase). These findings underscore the usefulness of the H2O-H2-CO2-CO-CH4 gas system and isotopic methods in tracking geothermal reservoir temperatures, their sources, and secondary processes, such as water reinjection or downflows from shallower aquifers.