Sensitivity of sea ice formation and dense shelf water production to perturbations of air temperature, precipitation, and wind stress in an important Antarctic coastal polynya system is investigated. Shelf water formation in the Mertz Glacier Polynya is a major source of Adélie Land Bottom Water. Coupled ocean and sea ice model simulations for 1996–1999 span a transitional period of the system: The 1996–1997 strong polynya state is characterized by high sea ice growth and export, ocean to atmosphere heat flux, shelf water density, and rate of dense water export; in the 1998–1999 weak polynya state all these quantities are greatly reduced. The 1990s interannual variability in air temperature and precipitation is of similar magnitude to future increases as projected for the Southern Ocean by the IPCC assessment. We model the polynya with perturbed climate change forcing and find that the system shows a reduction in shelf water export in both the strong/weak modes. Overall, the dense water export is reduced by 40% for a 2°C surface warming, and by 33% for a 20 cm a−1 precipitation increase. In the weak polynya state that is more likely in future climate, shelf water export is reduced by 81% for the warming and by 65% for the freshening. The reduction in dense shelf water export implies a corresponding reduction in Antarctic Bottom Water formation.