Indices based on branched glycerol dialkyl glycerol tetraethers (brGDGTs) have been useful in paleo-environmental reconstructions, although their applicability in river-estuarine sediments remains unclear. This study aims to investigate the correlation between brGDGT-based indices and modern environmental parameters, and to discuss possible impact factors. In this study, we discussed the applicability of several brGDGT-based indices, with specific interests on the IR_x’ (the relative abundance of 6- vs. 5-methylated brGDGTs) and CBT’ (cyclization index of branched tetraethers based on the separation of 5- and 6-methylated brGDGTs) for pH reconstruction, and MBT’_5ME (the methylation index of branched tetraethers based on the separation of 5- and 6-methylated brGDGTs) for MAAT (mean annual air temperature) reconstruction. From the Jiulong River (JLR) catchment, we have analyzed both riverbank soil samples and riverbed surface sediment samples for brGDGTs, with the following main findings: Firstly, for pH reconstruction, the indices CBT’ and IR_x’ are useful in soil and fluvial sedimentary settings. Secondly, for MAAT reconstruction, the MBT’_5ME index is sensitive to the air temperature, and the BayMBT₀ model performs relatively better than other global or regional calibrations in the study area; By employing the BayMBT₀ model, MAAT reconstructed from soils are higher than the measured MAAT, but are generally lower than the measured MAAT when reconstructed from riverbed surface sediments. Thirdly, the disagreement between the reconstructed results from the two sedimentary archives suggests that: Signatures of brGDGTs in the aquatic environment are under strong impacts of in situ produced brGDGTs; Impacts of upper-reach brGDGTs input might have resulted in the increasingly negative offset for the reconstructed MAAT downstream; And influences of complex aquatic biogeochemical conditions on sedimentary brGDGT signals are site-dependent in this area. Finally, brGDGT-based indices are sensitive to the source of brGDGTs, e.g., soil vs aquatic in situ brGDGTs; And terrigenous brGDGTs have been exposed to a range of complex biogeochemical processes before their deposition in the estuary. Based on these findings, we suggest that at least the above impact factors need to be taken into consideration when interpreting the brGDGT signals from estuarine archives, and thus, multi-proxy studies are encouraged. The findings of this study provide a better understanding of the correlation between brGDGT-based indices and modern environmental parameters in subtropical river systems, and provide useful information for interpreting the paleo-environmental signals based on brGDGTs from fluvial-estuarine archives.