Transport of organic carbon via rivers to estuary is a significant geochemical process in the global carbon cycle. This paper presents bulk total organic carbon (TOC) from the Dongjiang catchment to the adjacent Humen outlet, and discusses the applicability of δ ¹³C and ratio of carbon to nitrogen (C/N) as indicators for sources of organic matter in the surface sediments. Survey results showed that organic carbon concentration in summer were higher than in the winter. An elevated trend of TOC occurred along the river to the Humen outlet in both surveys, and the highest mean values of dissolved and particular organic carbon (DOC∼279 μmol L⁻¹ and POC∼163 μmol L⁻¹) were observed in the urban deltaic region in summer flood flow. Winter samples had a wide range of δ ¹³C and C/N (δ¹³C −24.6‰ to −30.0‰, C/N 4–13), and summer ones varied slightly (δ¹³C −24.2‰ to −27.6‰, C/N 6–18). As results suggest that POC in the three zones of upstream-delta-outlet dominantly came from riverbank soil, phytoplankton and agricultural C3 plants in winter, whereas main sources were from the riverbank and mangrove soil in summer. Moreover, anthropogenic sewage inputs had 11% and 7% contribution to POC in the deltaic and outlet. Transport accompanied with seasonal freshwater variation, phytoplankton production and degradation, and removal behavior caused variation of organic carbon concentration. The results also discovered that TOC export bulk in Dongjiang was approximately one quarter of Humen flux in the dry flow, and anthropogenic activity significantly impacted the river export contribution.