Nitrogen oxides affect health and climate. Their emissions, in the form of nitric oxide, from inland waters such as lakes are generally considered negligible and are absent in air quality and climate models. Here we find unexpected high emissions of nitric oxide from remote lakes on the Tibetan Plateau, based on satellite observations of tropospheric nitrogen dioxide vertical column densities and subsequent emission inversion at a fine resolution of 5 km. The total emissions from 135 lakes larger than 50 km2 reach 1.9 metric tons N h−1, comparable to anthropogenic emissions in individual megacities worldwide or the Tibet Autonomous Region. On average, the emissions per unit area reach 63.4 μg N m−2 h−1, exceeding those from crop fields. Such strong natural emissions from inland waters have not been reported, to the best of our knowledge. The emissions are derived from microbial processes in association with substantial warming and melting of glacier and permafrost on the plateau, constituting a previously unknown feedback between climate, lake ecology and nitrogen emissions. High-resolution satellite observations reveal that large lakes on the Tibetan Plateau have total nitric oxide emissions comparable to anthropogenic emissions from individual megacities worldwide.