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The Greenland ice sheet (GIS) is losing mass at an increasing rate due to surface melt and flow acceleration in outlet glaciers. Currently, there is a large disagreement between observed and simulated ice flow, which may arise from inaccurate parameterization of basal motion, subglacial hydrology or geothermal heat sources. Recently it was suggested that there may be a hidden heat source beneath GIS caused by a higher than expected geothermal heat flux (GHF) from the Earth’s interior. Here we present the first direct measurements of GHF from beneath a deep fjord basin in Northeast Greenland. Temperature and salinity time series (2005–2015) in the deep stagnant basin water are used to quantify a GHF of 93 ± 21 mW m −2  which confirm previous indirect estimated values below GIS. A compilation of heat flux recordings from Greenland show the existence of geothermal heat sources beneath GIS and could explain high glacial ice speed areas such as the Northeast Greenland ice stream.

High geothermal heat flux in close proximity to the Northeast Greenland Ice Stream