We examined membrane-spanning archaeal lipids using ultra high pressure liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) in a suite of sediment samples from both cored sequences (Messel oil shale and Lake Chala) and surface sediments (Azorean lakes) encompassing ancient and modern (Eocene to Present) lacustrine environments. Additionally we compared the lacustrine data to those of marine (Mediterranean cored sequences, Arabian Sea surface sediments and Monterey outcrop sediments) and hypersaline sediments (Vena del Gesso marls) as well as marine suspended particulate matter (SPM) from the Black Sea. Regular isoprenoidal glycerol dialkyl glycerol tetraethers (GDGTs) and glycerol dialkyl diethers (GDDs) were the most abundant membrane-spanning lipids in all investigated settings (>90 % and 84 % respectively). Interestingly, GDGTs with a cyclohexyl ring (S-GDGTs) were also present in almost all investigated lake sediments, in relative abundances of ca. 2–7 % and, for the first time, also their S-GDD counterparts were detected (2–10 %). The producers of S-GDGTs are still unknown, however our results show that it is likely that bottom water anoxia (both seasonally induced or permanent) is the driving factor for the production of these lipids, whereas previous studies suggested euxinia was required for production. Unsaturated GDGTs (uns-GDGTs, ca. 2 %) were only detected in Lake Chala sediments and surface sediments from Azorean lakes, but without accompanying uns-GDDs. GMGTs, glycerol monoalkyl glycerol tetraethers, were present in Messel oil shale and marine samples, while GMDs were only found in Messel oil shale.