Organic carbon (OC) in the estuary–coastal ocean continuum originates from multiple sources and is strongly influenced by land–ocean interactions. Hydrodynamic sorting and other processes play important roles in altering the distribution and fate of sedimentary OC during the transport. In this study, we applied carbon isotopes, biomarkers, and density fractionation in surface sediments from the Pearl River Estuary and adjacent coastal sea. The results showed that the sediments were dominated by high-density fractions (2.0–2.5 g cm⁻³ and >2.5 g cm⁻³), which also contained the majority of the total OC (TOC). The low-density fractions (<2.0 g cm⁻³) exhibited the highest TOC content and lignin concentration. With increasing density, TOC content decreased, whereas δ¹³C values progressively increased, indicating a growing contribution of marine-derived OC. A three-endmember mixing model based on δ¹³C and Λ₈ indicated that C₃ vascular plant-derived OC dominated the sediment fractions with densities <2.5 g cm⁻³. In contrast, soil-derived OC was the predominant component (52 ± 25%) in the >2.5 g cm⁻³ fraction. The contribution of marine-derived OC also increased progressively with sediment density. The Δ¹⁴C values ranged from −183‰ to −709‰ and displayed an initial increase followed by a decrease with increasing density. The low-density OC fraction was the most depleted in Δ¹⁴C. Lignin phenol derived degradation indices revealed selective degradation of lignin among the different density fractions, with greater degrees of degradation observed in the <2.0 g cm⁻³ and >2.5 g cm⁻³ fractions. These findings demonstrate that hydrodynamic sorting exerts a significant influence on the transport and degradation of OC from different sources and plays an important role in regulating the fate of organic carbon along the estuary–coastal ocean continuum.