The influence of floodplains on the composition and export of riverine dissolved organic matter (DOM) was investigated during 2009–2010 in the lower Mississippi River (MR) and its distributary, the Atchafalaya River (AR). The AR had significantly higher concentrations of dissolved organic carbon (DOC), chromophoric DOM (CDOM), total dissolved lignin phenols (TDLP), amino acids (TDAA), and neutral sugars (TDNS) than the MR. Syringyl to vanillyl phenol ratios in the AR were significantly lower, indicating greater contributions from gymnosperms (cypress) in AR floodplains. Higher DOC-normalized yields of CDOM and TDLP in the AR indicated a strong floodplain source of DOM. Compositions and yields of TDAA and TDNS suggested DOM in the AR was more bioavailable than that in the MR. Yields of CDOM and TDLP in the AR were highest during maximal litter fall, when the depletion in syringyl phenols was greatest. Significantly lower concentrations of total dissolved nitrogen observed in the AR were in part due to nitrogen removal in floodplains. Temporal variability in DOM composition was more pronounced in the AR than in the MR. These results demonstrate that floodplains have a major influence on the composition and concentrations of riverine DOM, and thereby on the fates of riverine DOM in coastal oceans. In 2009, over 40% of the DOC, TDLP, TDAA, and TDNS exported from the Mississippi-Atchafalaya River system was carried by the AR, indicating a more important role of the AR in DOM export than previously thought. Therefore, the AR should be considered in future studies of river impacts on coastal processes, such as coastal productivity and hypoxia in the northern Gulf of Mexico. Long-term (1996–2010) average DOC export from the AR and MR (0.90 and 1.72 Tg yr ⁻¹, respectively) indicates the Mississippi-Atchafalaya River system exports 0.7–1.0% of global riverine DOC. New estimates of DOC export provided here are critical to improve carbon budgets in the Gulf of Mexico.