Removal rate of $NO_3-N$ and TN in a free water surface wetland system with litter layer on its bottom was compared with that without one. The system was established on floodplain in the down reach of the Gwangju Stream in 2001. Its dimensions were 31 meters in length and 12 meters in width. Water of the stream was funneled into it and its effluent was discharged back into the channel. Average litter layer of 9.6 cm was formed on its bottom in 2007. The layer and above-ground parts of reeds and cattails on the system were eliminated in Spring 2008. Volumes and water quality of inflow and outflow of the system were analyzed from May to November in 2007 and 2008, respectively. Inflow into the system both in 2007 and 2008 averaged approximately $40m^3/day$ and hydraulic residence time both in 2007 and 2008 was about 1.5 days. Average influent $NO_3-N$ concentration in 2007 and 2008 was 2.16 and 2.05 mg/L, respectively and influent TN concentration in 2007 and 2008 averaged 3.98 and 3.89 mg/L, respectively. With a 0.05 significance level, effluent temperatures, influent concentrations of $NO_3-N$ and TN, and stem numbers per square meter and height of the emergent plants showed no difference between the system with litter layer and without one. $NO_3-N$ removal in the system with litter layer and without it averaged 55.59 and 46.06%, respectively and TN retention averaged 57.24 and 48.97%, respectively. Both $NO_3-N$ and TN abatement rates in the system with litter layer were significantly high (p < 0.001) when compared with those without one. The wetland system having litter layer on its bottom was more efficient for $NO_3-N$ and TN retention than that without one.