Fed by a complex network of rivers, the subglacial reservoirs force the overlying ice to rise and fall.
By tracking these changes with Nasa's Ice Cloud and land Elevation Satellite (ICESat) scientists were able to map the extent of the subglacial plumbing.
The results, published in the journal Science, show that some areas fell by up to 9m (30ft) over just two years.
"We didn't realise that the water under these ice streams was moving in such large quantities, and on such short time scales," said Dr Helen Fricker of the Scripps Institution of Oceanography, University of California, and one of the authors of the paper.
"We thought these changes took place over years and decades, but we are seeing large changes over months."
The results are important for understanding how the Antarctic Ice sheet, which contains nearly 90% of the world's ice, may respond to global warming and how much it may contribute to sea level rise.