Compound-specific isotope analysis (CSIA) has been used to assess the ability of δ13C signatures of fatty acid compounds to discriminate erosion sources in a rural Australian catchment. The study focussed on a high flow event (10-year recurrence interval) which occurred in the Logan–Albert catchment in January 2008, and augmented a previous sediment tracing study using fallout radionuclides and major/minor element geochemistry. It is found that surface soil from forest, pasture and cultivated land uses are well discriminated using CSIA. Furthermore, sub-surface soil sources associated with channel bank erosion and exposed subsoils (gullies and hillslope scalds) occurring specifically in the mid-western Logan catchment could also be discriminated. Selected fatty acid and bulk carbon δ13C data were used in the IsoSource mixing model to determine erosion sources contributing sediment. The results were compared with results obtained using other sediment tracers. For the lower Logan River, the CSIA tracing results are consistent with fallout radionuclide and element geochemistry tracing, with channel bank erosion being confirmed as the major sediment source. Moreover, CSIA has quantified the significant contribution of exposed subsoils originating on hillslopes and drainage lines from the mid-western region of the Logan catchment. In the Albert River catchment, about 40% of sediment comes from forest land use, although more than half of this may come from sub-surface sources. These results have demonstrated that CSIA has the potential to significantly enhance the ability of sediment tracing studies to determine the extent that different land uses and erosion processes are contributing eroded soil to rivers, allowing an assessment of soil erosion and transport model predictions. Copyright © 2012 John Wiley & Sons, Ltd.