Glycerol dialkyl glycerol tetraether (GDGT) membrane lipids of Archaea respond to gradients in temperature and pH; however, it is unclear how these lipids respond to gradients of other environmental variables. Here, we analysed water chemistry, archaeal lipids and amoA- and nirS genes from 37 Tibetan hot springs. Strong correlations between intact polar lipids and their degradation product core lipids indicate that these two pools of lipids are closely related and may be formed in situ in the hot springs. Cluster analysis resulted in three major groups, within each of which the individual samples showed better correlations between ring index or TEX86 (TetraEther Index of tetraethers with 86 carbons) and temperature, pH or geochemical variables (e.g. nitrite, phosphate) in the polar fraction than in the corresponding core fraction. Most of these relationships did not exist when all of the samples were considered as a whole. Abundances of amoA- and nirS genes were strongly correlated with some of the intact polar- or core lipids. Our results suggest link between specific microbial functions (e.g. ammonia oxidation or nitrite reduction) and the production of individual GDGT lipids and highlights the potential utility of GDGT lipids as proxies for biogeochemical processes.