Abundances and distributional changes of branched glycerol dialkyl glycerol tetraethers (brGDGTs) in fluvially influenced sediments are used in various paleoclimate studies to reconstruct variations in soil export, continental air temperature and soil pH in corresponding river basins. For accurate interpretation of these records, it is important to understand the provenance and the evolution of biomarker signals as they move through the river system. Here we investigate the brGDGT composition of modern river sediments of the Danube River, the second largest river in Europe. BrGDGT-based mean annual air temperature and soil pH parallel the actual values of air temperature and soil pH from the upper to the lower basin, showing that signals predominantly reflect local as opposed to basin-wide environmental conditions. Furthermore, data generated using the recently developed method with improved chromatography, separating the 6-methyl-isomers from the 5-methyl-isomers, was compared with that resulting from the conventional method. We show that the temperatures and pH values reconstructed using the data obtained by improved chromatography best resemble the local environmental conditions throughout the Danube River basin. Our results highlight the importance of in-depth studies within river systems to better understand the provenance of biomarker signals in fluvially derived sedimentary archives.