It has now been known for several years that a 200-km-long lake, called Lake Vostok, lies beneath the ice sheet on which sits Vostok Station in Antarctica1, 2, 3, 4, 5. The conditions at the base of the ice sheet above this subglacial lake can provide information about the environment within the lake, including the likelihood that it supports life2. Here we present an analysis of the ice-sheet structure from airborne 60-MHz radar studies, which indicates that distinct zones of basal ice loss and accretion occur at the ice–water interface. Subglacial melting and net ice loss occur in the north of the lake and across its 200-km-long western margin, whereas about 150 m of ice is gained by subglacial freezing in the south. This indicates that significant quantities of water are exchanged between the base of the ice sheet and the lake waters, which will enrich the lake with gas hydrates, cause sediment deposition and encourage circulation of the lake water.