The Pearl River Estuary (PRE), a large subtropical estuary under intensive anthropogenic pressure, was investigated for sedimentary organic carbon (OC) dynamics using surface sediments and cores collected during 2021–2022, combined with a two‑decade historical dataset (2001–2022). Over this period, total organic carbon (TOC) and total nitrogen (TN) showed no significant variations, indicating a dynamic burial equilibrium. However, significant positive trends in δ¹³C and δ¹⁵N (p < 0.05) reveal a systemic OC compositional shift: δ¹³C enrichment reflects reduced terrestrial export (due to watershed conservation and reservoir interception) alongside enhanced marine production fueled by nutrients; δ¹⁵N enrichment signals rising fertilizer/sewage inputs, amplified by estuarine denitrification. Spatially, a land‑to‑sea gradient shows terrigenous dominance in the inner Lingdingyang and marine dominance outer Lingdingyang. Quantitative two‑endmember mixing modeling estimated that marine‑derived OC comprised 54.5 ± 14.8% of surface sedimentary OC, significantly lower than the down‑core average of 64.5 ± 6.8%. This ~10% offset suggests a long‑term structural transformation—likely during the rapid industrialization of the 1980s–1990s—wherein the relative role of marine autochthonous production in sedimentary carbon burial diminished, while terrestrial inputs were maintained or even relatively enhanced. Carbon stocks and burial fluxes exhibited inverse patterns—outer Lingdingyang stored more carbon (61.7 t C ha⁻¹) with lower burial flux (26.6 g C·m⁻²·yr⁻¹), while Lingdingyang showed lower stocks (44.8 t C ha⁻¹) but higher burial flux (43.7 g C·m⁻²·yr⁻¹)—revealing functional complementarity between short-term burial hotspots and long-term stable reservoirs. Collectively, these findings demonstrate that apparent TOC stability masks a structural transformation in estuarine carbon cycling, underscoring the necessity of integrating source composition, burial flux, and stock metrics across multiple timescales to accurately assess carbon sink functions in human-impacted estuaries.