Lipid biomarkers have been extensively used to reconstruct paleoenvironmental conditions. However, the entrainment of local compounds from source to sink may complicate interpretations. Here we present: (i) glycerol dialkyl glycerol tetraether (GDGT) distributions from the Amazon River and its main tributaries (i.e. Japurá, Içá, Juruá, Jutaí, Madeira, Solimões, Negro, Tapajós and Purus); and (ii) GDGT distributions and n-alkane isotopic compositions of soils and sediments from the Xingu River, a large clearwater River in eastern Amazonia. Our study aimed at understanding the processes and patterns related to distinct GDGT distributions and n-alkane isotopic signatures across lowland Amazonia. Suspended sediment samples from the Amazon Basin were obtained during the low-water season of 2015. Soil and suspended sediment samples from the Xingu Basin were obtained during the low- and high-water seasons of 2011, 2012, 2016 and 2017. Riverbed material was obtained using a Van Veen bottom sampler. Suspended material was concentrated using a Merck Millipore Ultrafiltration system equipped with Pellicon 2 Ultrafiltration cassettes (0.45 μm, 0.5 m2) after pumping up to 100 L of water from 60% of the total water column.