Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are microbial molecular fossils ubiquitous in natural environments. The correlation between the Methylation Index of brGDGTs (the ${\mathrm{M}\mathrm{B}\mathrm{T}}_{5\mathrm{M}\mathrm{E}}^{\text{'}}$ paleothermometer) and temperature offers an important tool for reconstructing past terrestrial temperatures. However, factors other than temperature could also affect the distribution of brGDGTs in lacustrine systems, hampering the quantitative application of this paleothermometer. Here we investigated brGDGT distributions in contemporary sediments collected from 52 lakes in mid-latitude Asia. Combined with published brGDGT data from other lakes across the globe, we have found a strong salinity control on the relative abundance of 5-methyl brGDGTs versus their late-eluting isomers (including 6-methyl, 7-methyl, and unknown isomers). This allows the development of novel indices based on the isomerization of brGDGTs for tracing past lake water salinity. We also demonstrate that salinity-controlled isomerization of pentamethylated and hexamethylated brGDGTs can significantly impact the ${\mathrm{M}\mathrm{B}\mathrm{T}}_{5\mathrm{M}\mathrm{E}}^{\text{'}}$ paleothermometer, potentially leading to an overestimation of past temperature, but the temperature signal can be extracted out of the ${\mathrm{M}\mathrm{B}\mathrm{T}}_{5\mathrm{M}\mathrm{E}}^{\text{'}}$ index after correcting the salinity effect. As demonstrated in application to a Lake Qinghai (China) sediment core spanning the last 18 kyr, our finding could facilitate the simultaneous retrieval of reliable temperature and salinity records using brGDGTs in lacustrine settings, in particular for lakes that have experienced large salinity changes during the geological past.