Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are potentially valuable biomarkers for paleoclimatic and paleoenvironmental studies. However, multiple factors controlling their variations in lake sediments hamper the widespread application of brGDGT-based proxies. Here we investigate brGDGTs in water column suspended particulate matter (SPM) and surface sediments in a series of lakes with a wide range of depths from three main volcanic fields of northeastern China. The brGDGT distribution patterns from SPM and surface sediments of these lakes differ greatly from those of surrounding soils, indicating a predominant aquatic origin for brGDGTs. We find that the ratio of 5-methyl hexamethylated and pentamethylated brGDGTs with no cyclopentane rings (IIIa/(IIa + IIIa); designated as HP5) is strongly correlated with water depth. Re-examination of published brGDGT data from SPM samples in redox-stratified Lake Lugano reveals similar relationships, whereas such correlations are much weaker in Lake Superior which does not have an anoxic hypolimnion. Importantly, we find that there is strong correlation between HP5 and dissolved oxygen in water column of the redox-stratified lakes, suggesting that the observed apparent HP5–water depth correlation may be primarily attributed to depth-progressive shifts in the brGDGT-producing bacterial communities with different redox requirements (aerobic, facultative anaerobic, and anaerobic bacteria). Notably, brGDGT methylation indices (MBTʹ5ME and MBTʹ6ME) of surface sediments display poor correlations with air temperatures in our study lakes, calling for caution in applying MBTʹ5ME and MBTʹ6ME as temperature proxies in these lakes.