The existence of many subglacial lakes provides clear evidence for the widespread presence of water beneath the East Antarctic ice sheet, but the hydrology beneath this ice mass is poorly understood. Such knowledge is critical to understanding ice flow, basal water transfer to the ice margin, glacial landform development and subglacial lake habitats. Here we present ice-sheet surface elevation changes in central East Antarctica that we interpret to represent rapid discharge from a subglacial lake. Our observations indicate that during a period of 16 months, 1.8 km3 of water was transferred over 290 km to at least two other subglacial lakes. While viscous deformation of the ice roof above may moderate discharge, the intrinsic instability of such a system suggests that discharge events are a common mode of basal drainage. If large lakes, such as Lake Vostok or Lake Concordia, are pressurizing, it is possible that substantial discharges could reach the coast. Our observations conflict with expectations that subglacial lakes have long residence times and slow circulations, and we suggest that entire subglacial drainage basins may be flushed periodically. The rapid transfer of water between lakes would result in large-scale solute and microbe relocation, and drainage system contamination from in situ exploration is, therefore, a distinct risk.