Freshwater diversions from the lower Mississippi River into the region's wetlands have been considered an alternative means for reducing nitrogen loading. The Atchafalaya River Swamp, the largest freshwater swamp in North America, carries the entire discharge of the Red River and 30% of the discharge of the Mississippi River, but it is largely unknown how much nitrogen actually can be retained from the overflowing waters of the Mississippi-Atchafalaya River system. Nitrogen discharge from the upper Mississippi River Basin has been implicated as the major cause for the hypoxia in the Northern Gulf of Mexico, which threatens not only the aquatic ecosystem health, but also Louisiana's fishery industry, among other problems. This study was conducted to determine the change in organic nitrogen mass as water flows through the Atchafalaya River Swamp and into the Gulf of Mexico. By utilizing the river's long-term discharge and water quality data (1978-2002), monthly and annual organic nitrogen fluxes were quantified, and their relationships with the basin's hydrologic conditions were investigated. A total Kjeldahl nitrogen (TKN) mass input-output balance between the upstream (Simmesport) and downstream (Morgan City and Wax Lake Outlet) locations was established to examine the organic nitrogen removal potential for this large swamp. The results showed that on average, TKN input into the Atchafalaya was 200 323 tons year−1 and TKN output leaving the basin was 145 917 tons year-1, resulting in a 27% removal rate of organic nitrogen. Monthly TKN input and output in the basin were highest from March to June (input vs. output: 25 000 vs. 18 000 tons month-1) and lowest from August to November (8000 vs. 6000 tons month-1). There was a large variation in both annual and inter-annual organic nitrogen removals. The variability was positively correlated with the amount of inflow water at Simmesport, suggesting that regulating the river's inflow at the Old River flood control structures may help reduce nitrogen loading of the Mississippi River to the Gulf of Mexico. Furthermore, the in-stream loss of organic nitrogen indicates that previous studies may have overestimated nitrogen discharge from the Mississippi-Atchafalaya River system.