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Lake‐level reconstructions, related to terrestrial hydrological changes, are important for our understanding of past and future climates. Currently, however, reliable lake‐level proxies are still limited. Here we report distributions of archaeal tetraether lipids in 70 surface sediment samples collected from 55 lakes in midlatitude Asia. We have found that among various lake physico‐chemical characteristics, the relative abundances of crenarchaeol and Hydroxylated isoprenoid glycerol dialkyl glycerol tetraethers (%cren and %OH‐GDGTs) are best correlated with lake water depth, due to a preference of Thaumarchaeota, the producer of these biomarkers, for a niche in subsurface lake water. This supports the recent hypothesis based on single‐lake investigations that %cren and %OH‐GDGTs are potentially novel lake‐level proxies. Our results also suggest that %OH‐GDGTs is less affected by soil input than %cren. Nevertheless, other confounding factors should be well constrained and local/site‐specific calibrations are needed before the two molecular proxies are used quantitatively in down‐core applications.