Garnet from skarns exposed at Empire Mountain, Sierra Nevada (California, United States) batholith, have variable δ18O values including the lowest known δ18O values of skarn garnet (–4.0‰) in North America. Such values indicate that surface-derived meteoric water was a significant component of the fluid budget of the skarn-forming hydrothermal system, which developed in response to shallow emplacement (∼3.3 km) of the 109 Ma quartz diorite of Empire Mountain. Values of δ18O, measured in situ across single garnet crystals by secondary ion mass spectrometry, vary considerably (up to 7‰) and sometimes abruptly, indicating variable mixing of meteoric, magmatic, and metamorphic water. Brecciation in the skarns and alteration of the Empire Mountain pluton suggests that fracture-enhanced permeability was a critical control on the depth to which surface waters penetrated to form skarns and later alter the pluton. Compared to other Sierran systems, much greater volumes of skarn rock suggest an exceptionally vigorous hydrothermal system that saw unusually high levels of decarbonation reaction progress, likely a consequence of the magma intruding relatively cold wallrocks inboard of the main locus of magmatism in the Sierran arc at that time.