Glaciers in the upper Indus supply more than half of the river water, are experiencing significant melting with a debated fate. The recent melting rate is still contained by considerable uncertainties, hindering to estimate precise glacier mass change. Here we present geodetic mass balance results for the whole Indus Basin using SRTM and ALOS 30 m elevation data, improved glacier inventory, optimized glacier surface density, and validation through in-situ differential GPS and ICESat data. Our glacier inventory and derived by improving RGI6.0 boundaries and separated into debris cover and debris free parts. The derived surface elevation changes were converted into annual mass balances using separated density assumptions (four criteria) for debris-covered ice (900 ± 60 kg m−3), debris-free ice (below 20° and 25° slopes (850 ± 60 kg m−3) and above 20° and 25° slopes (600 ± 60 kg m−3)), respectively. The resulting mass balance biased between −0.20 and 0.09 m water equivalent (w.e.) a-1 using an average (850 ± 60 kg m−3) density assumption throughout the Indus Basin. In the western Himalaya and Hindu Kush, the glacier mass losses are less affected by the average density assumption compared to the Karakoram. The western (Hunza) and central (Shigar) Karakoram glaciers show negligible mass losses of −0.02 ± 0.12 and −0.01 ± 0.13 m w.e. a−1 in contrast to the relatively more negative mass balance (−0.26 ± 0.21 m w.e. a−1) in the eastern (Shyok) Karakoram. All the sub-basins exhibit negative mass balances, with the most negative values ranging from −0.34 ± 0.31 to 0.44 ± 0.27 m w.e. a−1 in the Ravi, Chenab and Jhelum sub-basins of the Himalaya. The whole Indus Basin contributes approximately +0.014 ± 0.016 mm a−1 to the global mean sea-level equivalent.