We report gas chromatography-isotope ratio monitoring-mass spectrometry (GC-IRM-MS) measurements of the δ13C values of individual biomarker compounds (n-alkanes) extracted from a 3 m marine sediment core taken near the mouth of the Johnstone River, North Queensland, Australia. The technique allows a purely terrestrial isotope signal to be discerned despite mixing of terrestrial and marine-derived carbon. The results indicate that there has been a 2% increase in the δ13C values of terrestrially derived n-alkanes (C29-C33) since clearing of the forested Johnstone River drainage basin for sugarcane and pasture began in the late 19th century. A much slower ∼1% increase in δ13C values after 6,000 years BP and prior to European settlement may be related to a decrease in rainfall in the basin, or to an increase in the abundance of C4 plants as a result of increased aboriginal burning. The results from the sediment core are consistent with data obtained for modern river sediments from forested and cleared subcatchments within the basin, and demonstrate that the δ13C values of terrestrially derived n-alkanes in the marine environment can be used to assess basin-wide vegetation changes in adjacent river catchments on geological timescales.