The thermal state of polar continental crust plays a crucial role for understanding the stability and thickness of large ice sheets, the visco-elastic response of the solid Earth due to unloading when large ice caps melt and, in turn, the accuracy of future sea-level rise prediction. Various studies demonstrate the need for precise measurements and estimation of geothermal heat flow (GHF) in Antarctica for better constrained boundary conditions to enhance the ice sheet model performance. This study provides ground-truth for regional indirect GHF estimates in the Amundsen Sea Embayment, which is part of the West Antarctic Rift System, by presenting in situ temperature measurements in continental shelf sediments. Our results show regionally elevated and heterogeneous GHF (mean of 65 mW m−2) in the Amundsen Sea Embayment. Considering thermal blanketing effects, induced by inflow of warmer water and sedimentary processes, the estimated GHF ranges between 65 mW m−2 and 95 mW m−2.