The bulk organic matter composition (total organic carbon (TOC) content and d13CTOC ) and composition of isoprenoid and branched glycerol dialkyl glycerol tetraethers (GDGT) in surface sediments from 43 stations in the Berau River delta (east Kalimantan, Indonesia), including two coast-shelf transects and stations within the river mouth, were examined to reveal the spatial heterogeneity in these parameters in order to assess the impact of a tropical river loaded with suspended matter on the sedimentary organic matter in the shelf system. The high-resolution study showed that, despite the extensive transport of eroded soil material by the river to the sea, terrestrial organic matter and brGDGTs are only deposited on a relatively small part of the shelf. The concentrations of brGDGTs are highest (up to 120 µg/g TOC) in sediments deposited in and close to the mouth of the Berau River and their distribution indicates that they represent a mixture of soil-derived and river in-situ produced brGDGTs. Crenarchaeol concentrations reach 700 µg/g TOC in sediments deposited on the outer shelf due to Thaumarchaeotal production in shelf waters. This results in a strong gradient (0.93-0.03) in the BIT index, with high values in the river mouth and low values on the shelf. The decline in the BIT index is caused by both decreasing concentrations of the brGDGTs and increasing concentrations of crenarchaeol. The BIT index shows a highly significant but non-linear relationship with d13CTOC. On the shelf, in the area not under the direct influence of the Berau River, cyclic brGDGTs become relatively dominant, most probably due to in-situ production in the alkaline pore waters of the surface sediments. The spatial heterogeneity of sources of brGDGTs on the Berau shelf complicates the use of brGDGTs as temperature proxies. Application of the global soil calibration to sedimentary mixtures of brGDGTs in the river-influenced area of the shelf results in a severe underestimation of mean annual air temperature (MAT) by 6 °C. This is due ...