During the Cenozoic, alkaline magmatism related to rifting in the Ross Sea embayment affected the basement of northern Victoria Land, Antarctica. Shallow intrusions supplied the necessary heat to cause groundwater circulation through permeable rocks, producing local hydrothermal systems. In the granitoid country rocks of the two adjacent areas of Mt. Monteagle and Mt. McGee, the biotite δD values range from −69‰ to −141‰ and from −66‰ to −183‰, respectively, and K-feldspars show δ18O values as low as 3.7‰ and 4.4‰. These values result from isotope exchange between igneous minerals and hydrothermal fluids with a dominant meteoric water component. Geological and tectonic histories of the two areas show marked similarities; therefore, different δ18O and δD values of hydrothermally altered rocks may be interpreted in terms of different isotopic composition of the waters feeding the hydrothermal systems. The isotopic shift of these meteoric waters indicates that climate change occurred in the time span between the 42 Ma intrusion of Mt. Monteagle and the 38 Ma intrusion of Mt. McGee, thus suggesting a cooling episode in the Ross Sea region during late Eocene time.