The photosynthetic conversion of dissolved inorganic carbon (DIC) into organic carbon (OC) by using aquatic phototrophs in rivers may serve as a potential carbon sink, especially in the carbonate rock areas, thereby offering a clue for finding the missing carbon sink. However, primary-produced autochthonous OC is erroneously considered as terrestrial-derived allochthonous OC. Thus, carbonate weathering-related carbon sink is underestimated if only DIC concentrations sampled at river mouths are considered, and the transformation of DIC to autochthonous OC is neglected. Therefore, distinguishing sources of autochthonous and allochthonous OC is vital in the assessment of carbon sink. In this study, source-specific biomarkers, in association with chemical compositions and phytoplankton proxies in water samples collected from the Pearl River, were analyzed to determine OC sources. Results showed that biomarkers in the Pearl River were quite abundant, and the calculated average autochthonous OC was approximately 65% of the total OC, indicating intense in-river primary productivity. Moreover, phytoplankton biomass and DIC concentration were positively related, indicating the DIC fertilization effect on aquatic photosynthesis. High total suspended solid (TSS) on the water surface blocked the sunlight and then reduced phytoplankton production. However, in situ photosynthesis of phytoplankton could also produce autochthonous OC, even larger than the allochthonous source at sites with high DIC, and even with higher TSS concentrations. These findings comprehensively elucidated the formation of autochthonous OC based on the coupling action of rock weathering and photosynthetic activity in the riverine system, suggesting a potential direction for finding the missing carbon sink. (C) 2016 Elsevier Ltd. All rights reserved.