The composition and fluxes of organic carbon transported by river systems are important for the terrestrial carbon cycle in terms of source to sink, and the impacts of dam regulation on large rivers are well documented. However, complex river–lake interactions and extreme weather events still hinder a comprehensive understanding of the transformation of riverine carbon within the large river basin. This study investigated particulate organic matter during the 2012 flood in the Changjiang Basin (CJB) and collected suspended particles from the mainstream of the CJB, Dongting and Poyang lakes. The amount, grain size, particulate organic carbon (POC) content, chlorophyll a (Chl-a), and lignin phenols of samples were measured. The results indicate that soil is the primary source of POC in lake-unaffected stations (46.9%–86.9%), while lake-affected stations exhibit significant contributions from phytoplankton (41.4%–78%). Notable alterations in the composition of terrestrial organic carbon occur during its transfer from soil to the river and from the upper to the lower reaches. Comparing the POC characteristics in the Changjiang across various years and hydrological conditions reveals that the characterization of POC in the Changjiang during flooding is mainly influenced by the dams. Another notable finding is that Dongting and Poyang lakes intercepted sediment and transported algae-rich organic matter to the mainstream. This process potentially converts the middle reaches of the Changjiang into a carbon source. River-lake interactions are complex and affected by lake morphology and flooding events. This study enhances our understanding of biogeochemical processes in dam-regulated rivers under extreme weather conditions, and emphasizes the importance of river–lake interactions for the transformation and transportation of riverine organic carbon in large fluvial system.
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