•GDGTs in soil showed depth variation in concentration and composition.•The br and iso GDGTs were abundant in the top and subsurface, respectively.•In situ production of br GDGTs in lake water is suggested.•CBT and MBT′ values for lake sediments corresponded to lake water pH and temperature.We investigated glycerol dialkyl glycerol tetraether (GDGT) distributions in soils and river/lake sediments in the Lake Biwa basin of central Japan, in order to understand their source and fate in a terrigenous environment. GDGTs in 16 soil profiles exhibited significant depth variation at each site. Branched (br) GDGTs were generally most abundant in the surface litter layer (O layer) and decreased with depth, while the maximum concentration of crenarcheol appeared in the upper soil layer (A layer), above the maximum concentration of the other isoprenoid (iso) GDGTs. The finding is consistent with different microbial communities contributing to the GDGT pools of the subsurface soil sequences. The relationship between methylation index of br tetraethers/cyclization ratio of br tetraethers (MBT′/CBT) and pH/mean annual air temperature (MAAT) for Lake Biwa basin soils was consistent with that found in global soil samples. The GDGT distributions in surface sediments from the lake differed from those in soils and river sediments in the watershed, suggesting that the GDGTs were produced in the lake water rather than supplied from the land. The CBT for lake sediments from different water depths corresponded to water pH values. We thus infer that the CBT for lake sediments may serve as proxy for lake water pH and can be applied to paleoenvironmental reconstruction.