An extensive perennial firn aquifer was previously mapped in Helheim Glacier, Southeast Greenland. However, critical constraints on aquifer thickness have been so far unobtainable without expensive field observations. Here we present a novel method that combines very high frequency airborne deep ice radar and ice sheet modeling to retrieve aquifer thickness and its evolution at Helheim Glacier. Using 2012–2014 radar measurements, we identify three aquifers of 4–25 m thick, with a total area of 1,934 km$^2$ and water storage of 2.2 ± 1.5 Gt, about half the volume of previous estimates. The aquifer system is dynamic, and its thickness varies interannually at a rate similar to changes in surface mass balance. The rapid upstream migration of the saturated aquifer implies that this feature has the potential to increase its storage potential in upper Greenland. Together, a combination of very high‐ and ultra high frequency radar sounding provides a powerful tool to characterize englacial firn aquifers.