Through the detection of surface deformation in response to water movement, recent satellite studies have demonstrated the existence of subglacial lakes in Antarctica that fill and drain on timescales of months to years. These studies, however, were confined to specific regions of the ice sheet. Here we present the first comprehensive study of these ‘active’ lakes for the Antarctic ice sheet north of 86° S, based on 4.5 years (2003–08) of NASA’s Ice, Cloud and land Elevation Satellite (ICESat) laser altimeter data. Our analysis has detected 124 lakes that were active during this period, and we estimate volume changes for each lake. The ICESat-detected lakes are prevalent in coastal Antarctica, and are present under most of the largest ice-stream catchments. Lakes sometimes appear to transfer water from one to another, but also often exchange water with distributed sources undetectable by ICESat, suggesting that the lakes may provide water to or withdraw water from the hydrologic systems that lubricate glacier flow. Thus, these reservoirs may contribute pulses of water to produce rapid temporal changes in glacier speeds, but also may withdraw water at other times to slow flow.