The data set contains concentration data of the source-specific low-temperature biomass burning tracer levoglucosan from riverbed and suspended sediments from the Amazon River System and marine surface sediments from the tropical Atlantic Ocean. Both riverine and marine sample material consists of modern sediments. The data was measured in 2017 at the Royal Netherlands Institute for Sea Research (NIOZ) using an Agilent 1290 Infinity Ultra-high performance liquid chromatographer (UHPLC) coupled to an Agilent 6230 Time-Of-Flight (TOF) mass spectrometer. The purpose of the measurements was to assess the transport and deposition of low-temperature pyrogenic carbon in the Amazon River System and adjacent marine deposition areas.