To better understand the long-term climate history of Antarctica, we studied Lake Bonney in Taylor Valley, Southern Victoria Land (78?? S). Helium isotope ratios and He, Ne, Ar and N2 concentration data, obtained from hydrocasts in the East (ELB) and West (WLB) Lobesof Lake Bonney, provided important constraints on the lake's Holocene evolution. Based on very low concentrations of Ar and N2 in the ELB bottom waters, ELB was free of ice until 200 ?? 50 years ago. After which, low salinity water flowing over the sill from WLB to ELB, covered ELB and formed a perennial ice cover, inhibiting the exchange of gases with the atmosphere. In contrast to the ELB, the WLB retained an ice cover through the Holocene. The brine in the WLB bottom waters has meteoric N2 and Ar gas concentrations indicating that it has not been significantly modified by atmospheric exchange or ice formation. The helium concentrations in the deep water of WLB are the highest measured in non-thermal surface water. By fitting a diffusional loss to the 3He/4He, helium, and Cl profiles, we calculate a time of ???3000 years for the initiation of flow over the sill separating the East and West Lobes. To supply this flux of helium to the lake, a helium-rich sediment beneath the lake must be providing the helium by diffusion. If at any time during the last million years the ice cover left WLB, there would be insufficient helium available to provide the current flux to WLB. The variations in water levels in Lake Bonney can be related to climatic events that have been documented within the Southern Victoria Land region and indicate that the lakes respond significantly to regional and, perhaps, global climate forcing. ?? 2004 Kluwer Academic Publishers.