To understand the movement of subglacial water in Antarctica, we present an updated inventory of active subglacial lakes using ICESat-2 laser altimetry data. The ICESat-2/ATLAS instrument’s six-beam laser array captures denser point measurements than the previous generation ICESat and Cryosat-2 satellites, allowing us to examine the spatial and temporal variability of active subglacial lakes with unprecedented detail. Active subglacial lakes are classified directly from the high density ATL11 land ice time-series (60 m along track spatial resolution) point cloud data using an unsupervised density-based clustering algorithm. The key finding we show is how subglacial lake shorelines can migrate spatially over time through fill-drain cycles. In addition, we examine subglacial water connectivity from coupled fill-drain cycles over lakes at the Whillans Ice Stream on the Siple Coast. This study yields new insights into the dynamic nature of the subglacial water system in Antarctica, and will be of interest to biologists quantifying biogeochemical cycle processes and glaciologists studying the influence of subglacial hydrology on ice dynamics.