Biomarker-based climate proxies enable climate and environmental reconstructions for regions where other paleoclimatic approaches are unsuitable. The Antarctic Cenozoic record consists of widely varying lithologies, deposited in rapidly changing depositional settings, with large lateral variations. Previous sedimentological and microfossil studies indicate that the incorporation of reworked older material frequently occurs in these sediments, highlighting the need for an assessment of biomarker distribution across a range of depositional settings and ages to assess the role reworking may have on biomarker-based reconstructions. Here, we compare sedimentary facies with the distribution of n-alkanes and hopanoids within a terrestrial outcrop, two glaciomarine cores and a deep sea core, spanning the Late Oligocene to Miocene in the Ross Sea. Comparisons are also made with n-alkane distributions in Eocene glacial erratics and Mesozoic Beacon Supergroup sediments, which are both potential sources of reworked material. The dominant n-alkane chain length shifts from n-C29 to n-C27 between the Late Eocene and the Oligocene. This shift is likely due to changing plant community composition and the plastic response of n-alkanes to climate cooling. Samples from glaciofluvial environments onshore, and subglacial and ice-proximal environments offshore are more likely to display reworked n-alkane distributions, whereas, samples from lower-energy, lacustrine and ice-distal marine environments predominantly yield immature/contemporaneous n-alkanes. These findings emphasise that careful comparisons with sedimentological and paleontological indicators are essential when applying and interpreting n-alkane-based and other biomarker-based proxies in glacially-influenced settings.