Archaeal glycerol dialkyl glycerol tetraethers (GDGTs) are increasingly popular and versatile tool for palaeolimnology studies, but their applications in paleohydrology are scarce, especially for thaumarchaeol which is specific for the newly proposed phylum Thaumarchaeota. After investigating our published GDGT data of Lake Qinghai, we found that both the concentration of thaumarchaeol and the relative abundance of thaumarchaeol to total archaeal GDGTs (%thaum) in core-top sediments increased significantly with increasing water depth (R=0.88 and 0.95, respectively), with lower concentrations of 5+/-5 ng/g in shallow areas (water depth<5m) and higher concentrations of 121+/-65ng/g in deep areas (water depth>10m). This is likely because that the producers of thaumarchaeol, Thaumarchaeota, prefer living in the relative deeper zone in lacustrine systems, where probably both competition of ammonium (the substrate) from other microbes and light intensity are low. Therefore, we proposed that thaumarchaeol was mainly produced in situ and changes in % thaum might reflect water-depth variations in this closed-basin lake. The application of % thaum as a water-depth indicator in a Holocene sediment sequence of core QH-2011 provided a high-resolution relative lake-level history of Lake Qinghai which resembles that inferred from the delta C-13(org) value obtained in the same core. This supports the use of %thaumas an indicator of lakewater depth in paleohydrology studies, especially for medium lakes. Moreover, the records of the two independent proxies in core QH-2011 confirmed a shallow Lake Qinghai in the early Holocene and a late-Holocene highstand, highlighting the importance of local temperature (and evaporation loss) in controlling effective moisture in the arid/semi-arid region.