Chromophoric dissolved organic matter (CDOM) exported from riverine catchments can influence biogeochemical processes in coastal environments with implications for water quality and carbon budget. Despite recent efforts to quantify C fluxes during high flow events, knowledge gaps exist regarding the fluxes and yield of terrestrial, reactive vs. recalcitrant CDOM under episodic to base-flow conditions from uplands to downstream estuaries. We used stream dissolved organic carbon (DOC) concentrations and CDOM optical properties using parallel factor analysis to characterize composition and fluxes under variable flow conditions for a coastal river basin in the SE USA. Our findings showed that episodic flows (>75th percentile) were marked by the elevated flux of humic acid-like CDOM and lower in-stream autochthonous production, or microbial degradation. Further, 70% of the terrestrial CDOM was exported during high flows, with a 3-fold increase in CDOM flux during episodic events, including Hurricane Irene in 2011. While, low flows (<25th percentile) were marked by an increased abundance of microbial, humic CDOM that can be easily processed within the estuary. Due to greater wetland coverage in the Neuse, the annual CDOM yield was 5–6 times higher than the larger rivers, such as the Mississippi, USA, and Changjiang, China. We suggest that similar coastal watersheds in SE USA or elsewhere may contribute substantial amounts of reactive CDOM to the estuaries during high flow conditions and can have negative water quality implications for the coastal C dynamics. These findings can help predict the evolution of coastal C cycling under projected climate change and inform the development of appropriate management strategies.