Abstract Atmospheric rivers (ARs) have the potential to generate large-impact hydrometeorological events over mountainous topography. In this study, we investigate ARs’ impacts on the hydrology of Indus basin (IB) and Ganga basin (GB), two highly populated basins of the Himalayas. We used the recently developed 37-yr-long ERA5-based AR database over the Himalayas to explore the influence of ARs on total and extreme precipitation, snowfall, and floods over these basins. We find that ARs contribute ∼25% to the annual rainfall in the IB and ∼15% in the GB. Over the mountainous regions, ARs contribute more than 50% to winter precipitation in Karakoram (KA), Hindu–Kush (HK), central (CH), and western Himalayas (WH), and respectively explain over 75%, 57%, 42%, and 30% of their interannual variability. The seasonal rainfall extremes over the mountain foothills are most often (50%–100%) associated with ARs in winter and spring, whereas the summer and autumn extremes over the plains and mountains foothills appear moderately associated with ARs (10%–40%). The two most catastrophic flood events (2014 Kashmir flood and 2013 Uttarakhand flood) in these basins are found to be linked with category 5 ARs. Upon further examination of floods over a long period, we noted that 56% and 73% of the floods in IB and GB, respectively, are related to ARs. Thus, our results establish that the variance of ARs is a major source of hydroclimate variability in the two Himalayan basins.