Understanding the transport of branched glycerol dialkyl glycerol tetraethers (brGDGTs) along the soil-river-lake transect is of vital importance, which helps discriminate the autochthonous from allochthonous contribution of brGDGTs in lake and river environment and favors the application of brGDGT-based proxies in paleo-reconstruction. We collected the sediment samples from the Qinghai Lake, the largest saline lake in China, as well as the river sediments and catchment soils, to examine the difference in the distribution of 5- vs. 6-methyl brGDGTs along the soil-river-lake transect. The brGDGT distributions were found to show a large variation along the transect, which can be reflected by the MBTʹ-derived indices and IR indices. There is a considerable difference in brGDGT distributions between soil and the river sediment. The inflowing rivers likely receive terrestrial brGDGT input to a variable degree. BrGDGTs in the Buha river are primarily of autochthonous origin whereas other ephemeral streams, like the Heima river, exhibit a similar brGDGT distribution to the surrounding soils, reflecting that these compounds are likely derived from soils. A higher quantity of 6-methyl brGDGTs and brGDGT-Ia was observed in the lake than in the river sediments, pointing to a preferential degradation of 5-methyl brGDGTs and/or an increase of in situ production of 6-methyl brGDGTs in the lake. In addition, in arid and alkaline soils, both CBTʹ and IR indices have strong correlations with soil pH even within the narrow pH range. Furthermore, we find a clear relationship of CBT with water salinity in Buha river. The difference in soil and river leads to a complicated interpretation for the CBT (CBTʹ) index. In the lake, the MBTʹ (specially represented by MBTʹ_5ME and MBTʹ_6ME), defined mainly by the fractional abundance of GDGT-Ia, increases with lake water depth, suggesting the maximum water depth is likely to impact the use of MBTʹ/CBT proxy in the Qinghai Lake.