Antarctica’s fast-flowing ice streams drain the ice sheet, with their velocity modulated by subglacial water systems. Current knowledge of these water systems is limited to the shallow portions near the ice-bed interface, but hypothesized deeper groundwater could also influence ice streaming. Here, we use magnetotelluric and passive seismic data from Whillans Ice Stream, West Antarctica, to provide the first observations of deep sub–ice stream groundwater. Our data reveal a volume of groundwater within a >1-kilometer-thick sedimentary basin that is more than an order of magnitude larger than the known subglacial system. A vertical salinity gradient indicates exchange between paleo seawater at depth and contemporary basal meltwater above. Our results provide new constraints for subglacial water systems that affect ice streaming and subglacial biogeochemical processes.