Alterations to the lower Mississippi River-floodplain ecosystem to facilitate commercial navigation and to reduce flooding of agricultural lands and communities in the historic floodplain have changed the hydrologic regime. As a result, the flood pulse usually has a lower water level, is of shorter duration, has colder water temperatures, and a smaller area of floodplain is inundated. Using average hydrologic conditions and water temperatures, we used established nitrogen and phosphorus processes in soils, an aquatic ecosystem model, and fish bioenergetic models to provide approximations of nitrogen and phosphorus flux in Mississippi River flood waters for the present conditions of a 2-month (mid-March to mid-May) flood pulse and for a 3-month (mid-March to mid-June), historic flood pulse. We estimated that the soils and aquatic biota can remove or sequester 542 and 976 kg nitrogen ha^-1 during the present and historic hydrologic conditions, respectively. Phosphorus, on the other hand, will be added to the water largely as a result of anaerobic soil conditions but moderated by biological uptake by aquatic biota during both present and historic hydrologic conditions. The floodplain and associated water bodies may provide an important management opportunity for reducing downstream transport of nitrogen in Mississippi River waters. ?? 2009, The Society of Wetland Scientists.