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Nitrogen removal efficiency is one of the major focuses in the application of animal wastewater to wetland systems. Nitrification and denitrification are the two major nitrogen transformation processes that require aerobic and anaerobic conditions respectively, for maximum transformation rates. Providing aerobic and anaerobic conditions alternatively would help maximize the nitrogen transformation and hence removal from wetlands. The frequency of keeping the wetland system dry (primarily aerobic) and wet (primarily anaerobic) becomes a critical aspect in maximizing nitrogen removal. Using a commercial nitrogen source resulted in 50% TN removal for 1:1 (weeks) hydroperiod (wet:dry) that was significantly different (= 0.05) from the 25% removal when continuously loaded. The average TKN accumulated in the cattails biomass was 50% more in hydroperiod ratio of 1:1 compared to when continuously wetted. A mass balance analysis of TN for each of the three tests where knot grass was grown revealed that nitrogen was actually being retained, transformed and ultimately lost from the system at significantly higher (=0.05) rates (67%) in systems subjected to high frequency, short stage duration hydroperiods when compared to the low frequency, long duration (47%) and continuously flooded systems (16%). Therefore, if maximum nitrogen removal is designed from a wetland system treating wastewater, installing a unit that is operated with a wetting and drying cycle of 1:1 week would be more beneficial as compared to a continuously wet system.