The effect of seasonal inundation on the decomposition of emergent macrophyte litter (Scolochloa festucacea) was examined under experimental flooding regimes in a northern prairie marsh. Stem and leaf litter was subjected to six aboveground inundation treatments (ranging from never flooded to flooded April through October) and two belowground treatments (nonflooded and flooded April to August). Flooding increased the rate of mass loss from litter aboveground but retarded decay belowground. Aboveground, N concentration decreased and subsequently increased earlier in the longer flooded treatments, indicating that flooding decreased the time that litter remained in the leaching and immobilization phases of decay. Belowground, both flooded and nonflooded litter showed an initial rapid loss of N, but concentration and percent of original N remaining were greater in the nonflooded marsh throughout the first year. This suggested that more N was immobilized on litter under the nonflooded, more oxidizing soil conditions. Both N concentration and percent N remaining of belowground litter were greater in the flooded than the nonflooded marsh the second year, suggesting that N immobilization was enhanced after water-level drawdown. These results suggest different mechanisms by which flooding affects decomposition in different wetland environments. On the soil surface where oxygen is readily available, flooding accelerates decomposition by increasing moisture. Belowground, flooding creates anoxic conditions that slow decay. The typical hydrologic pattern in seasonally flooded prairie marshes of spring flooding followed by water-level drawdown in summer may maximize system decomposition rates by allowing rapid decomposition aboveground in standing water and by annually alleviating soil anoxia.