Two intense rainfalls [Hurricane Joaquin (2015) and Hurricane Matthew (2016)], one year apart, provided a unique opportunity to examine changes in dissolved organic matter (DOM) dynamics in coastal blackwater rivers under extreme flooding conditions in the southeastern United States. Two sites along Waccamaw River (a coastal blackwater river) and the outflow of 18 sub-basins of Yadkin-Pee Dee Basin were sampled during and after the flooding events. The peaks of dissolved organic carbon (DOC) and nitrogen (DON) concentrations were observed 18 and 23 days after peak discharge in 2015 and 2016, respectively. Moreover, DOM aromaticity and abundance of humic substances significantly increased during the same period. Separation of discharge hydrograph into surface runoff and subsurface flow suggested that temporal changes were mainly due to contributions from subsurface flow flushing organic matter from wetlands and organic-rich riparian zones. The spatial analysis highlighted the key role of the forested wetlands as the only land use that significantly correlated with both DOM quantity (DOC and DON load) and DOM composition (i.e., aromaticity). The Yadkin-Pee Dee River basin alone exported more than 474 million kg DOC into the ocean during high-flow conditions from the 2016 event, indicating that such extreme short-term events mobilized enormous amounts of organic carbon and nitrogen to the ocean. Considering the predicted increase in frequency and intensity of extreme rainfall events in the eastern U.S., the results of this study can shed light on changes in DOM dynamics that may occur under such conditions in the near future.