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. Plain Language Summary Along the accumulation zone of the Greenland ice sheet, meltwater generated at the ice surface can infiltrate porous snow and firn and produce englacial aquifers. Thus far, early studies have mapped the extent of firn aquifers using a combination of ground-based and snow accumulation radar sounders. However, because englacial water can create additional attenuation for ice-penetrating radar systems, critical constraints on aquifer thickness have been so far unobtainable without logistical intensive field observations. Here we design a novel method that combines deep ice radar sounding and ice sheet modeling to overcome this challenge. We apply this technique to Helheim Glacier and find three aquifers of 4-25 m thick that changes over time with climate. Together, the combination of deep ice and snow accumulation radar sounding provides a powerful method to the understanding of the role of firn aquifers in Greenland Ice Sheet.