Nitrogen (N) has been linked to increasing eutrophication in the Gulf of Mexico and as a result there is increased interest in managing and improving water quality in the Mississippi River system. Water level reductions, or 'drawdowns', are being used more frequently in large river impoundments to improve vegetation growth and sediment compaction. We selected two areas of the Upper Mississippi River system (Navigation Pool 8 and Swan Lake) to examine the effects of water level drawdown on N dynamics. Navigation Pool 8 experienced summer drawdowns in 2001 and 2002. Certain areas of Swan Lake have been drawn down annually since the early 1970s where as other areas have remained inundated. In the 2002 Pool 8 study we determined the effects of sediment drying and rewetting resulting from water level drawdown on (1) patterns of sediment nitrification and denitrification and (2) concentrations of sediment and surface water total N (TN), nitrate, and ammonium (NH4+). In 2001, we only examined sediment NH4+ and TN. In the Swan Lake study, we determined the long-term effects of water level drawdowns on concentrations of sediment NH4+ and TN in sediments that dried annually and those that remained inundated. Sediment NH4+ decreased significantly in the Pool 8 studies during periods of desiccation, although there were no consistent trends in nitrification and denitrification or a reduction in total sediment N. Ammonium in sediments that have dried annually in Swan Lake appeared lower but was not significantly different from sediments that remain wet. The reduction in sediment NH4+ in parts of Pool 8 was likely a result of increased plant growth and N assimilation, which is then redeposited back to the sediment surface upon plant senescence. Similarly, the Swan Lake study suggested that drawdowns do not result in long term reduction in sediment N. Water level drawdowns may actually reduce water retention time and river-floodplain connectivity, while promoting significant accumulation of organic N. These results indicate that water level drawdowns are probably not an effective means of removing N from the Upper Mississippi River system.