The continent-wide hydrologic system below the Antarctic Ice Sheet helps regulate ice sheet dynamics and controls the biogeochemical fluxes from the continent to the Southern Ocean. Yet, the paucity of well dated, long-term records describing the evolution of Antarctic subglacial meltwater flow on centennial to millennial scales limits our ability to test potential feedbacks between ice motion, climate, and basal hydrology. Here we present a ten-thousand-year record of basal water dynamics and chemistry from ~110 ka sediment-bearing calcite precipitates that formed beneath the East Antarctic Ice Sheet during MIS 5e. Time series of sediment frequency and grain size indicate that subglacial meltwater flushing becomes more vigorous within decades of millennial-scale Southern Hemisphere warming events. Similarly, shifts in calcite geochemical composition record climate-driven changes in subglacial water provenance during these warm periods. The synchronized and sustained (>1 ka) changes in Antarctic basal hydrology with climate indicate rapid impact of climate forcing on subglacial water drainage systems. This connection between climate change and Antarctic basal hydrologic flow represents a potentially important feedback that can affect ice volume and nutrient discharge to the Southern Ocean on geologic timescales.