High mountain lakes are biodiversity treasures. They host endemic taxa, adapted to live in extreme environments. Among adaptations, production of diapausing eggs allows for overcoming the cold season. These diapausing eggs can rest in the sediments, providing a biotic reservoir known as an egg bank. Here, we estimated changes in abundance of the egg bank in two lakes in the Khumbu Region of the Himalayas, during the last ca. 1100 and 500 years, respectively, by analyzing two sediment cores. We tested viability of the diapausing eggs extracted from different layers of the sediment cores under laboratory conditions. We found that only diapausing eggs of the Monogont rotifer Hexarthra bulgarica nepalensis were able to hatch, thus suggesting that a permanent egg bank is lacking for the other taxa of the lakes, not least for the two Daphnia species described from these sites. Our results confirm previous studies suggesting that in high mountain lakes, the production of diapausing is mainly devoted to seasonal recruitment, therefore leading to a nonpermanent egg bank. The different ability of different taxa to leave viable diapausing eggs in the sediments of high mountain lakes therefore poses serious constraints to capability of buffering risk of biodiversity loss in these extremely fragile environments.