The potential influences of the increased anthropogenic stress during the Anthropocene have led to a focus on the sedimentary record in lake and estuary environments. In this study, the spatio-temporal occurrence of 16 polycyclic aromatic hydrocarbons (PAHs) and the n-alkanes from nC12–nC37 associated with organic groups (i.e., organic nitrogen (ON), organic carbon (OC), organic hydrogen (OH), and organic sulfur (OS)) in the 210Pb-dated estuary sediments of Poyang Lake were investigated and their sources and impacts were traced. The ON, OC, OS, and OH contents in the sediment cores ranged between 0.12 − 0.65%, 1 − 7.95%, 0.01 − 0.82%, and 0.03 − 1%, respectively. The age of estuarine sediment cores in Poyang Lake was measured to be 1885–2019 by the 210Pb-dating method. The 133-year sediment deposition occurred over different stages, each with its own characteristics. The PAH fluxes were in the range of 787.65–11269.18 ng cm− 2 a− 1. The high-ring PAHs were dominant, accounting for 74.02% of the total, and the main sources were biomass combustion and automobile exhaust emissions from 1885–2019 without marked change. On a centennial scale, the main n-alkane peaks were nC15, nC31, and nC33, which had an obvious odd-even predominance. The deposition flux of Σn-alkanes varied within the range of 10.33 − 213.86 µg cm− 2 a− 1. The long-chain monomers were dominant, and were found to originate from herbs. The environmental indicator analysis revealed that the restoration of forests and eutrophication of water bodies caused by human activities and a climate change from wet to drought conditions contributed to the relative contribution of autochthonous organisms and vascular plants during 1886–2019.