Abstract: As a part of surface runoff under terrestrial conditions, rivers could not only carry the terrestrial-derived isoprenoid glycerol dialkyl glycerol tetraethers (isoGDGTs), but also in-situ produced isoGDGTs to the lake. The features of isoGDGTs which come from in-situ archaea in the river were investigated to find out their potential impact on the application of the TEX₈₆ index of isoGDGTs in lacustrine environment. We took the Lake Fuxian basin in Southwest China as the research object and analyzed various samples collected around the lake, including surface soils, surface river sediments and year-round suspended particulate matters (SPM) in surface water. The results showed that isoGDGTs in SPM and soils were mainly originated from the cluster of Group I.1a Thaumarchaeota and Group I.1b Thaumarchaeota, respectively. The surface river sediments held a significant characteristic of in-situ anaerobic methanogenic archaea (e.g., Methanonatronarchaeia). Moreover, the abundance of archaeol in surface river sediments was significantly positively correlated with GDGT-1 abundance. It meant the anaerobic methanogenic archaea could contribute a higher abundance of GDGT-1 to distort the TEX₈₆ signal, further, which might result in the TEX₈₆ value of surface river sediments being apparently lower than that of soil. Furthermore, the above effects only occurred during the rainy season.