Wetland is important as a source of nitrous oxide (N2O), which depends on groundwater and anaerobic conditions involved for denitrification in the aquifer. In order to study the behavior of N2O in wetland, a typical headwater wetland has been chosen in Ichikawa, Chiba prefecture, Japan. It was found that N2O fluxes were high at the sides of valley where groundwater flowed in with high concentration of nitrate, and less than 0.045 mg N m–2 h–1 in the wetland where groundwater was almost free of nitrite. Also, the concentration of dissolved N2O in groundwater ranged from 0.78 to 80.5 μg N L–1 in the study area. Based on the spatial distributions of nitrate, dissolved N2O, hydraulic head, temperature, dissolved oxygen, and oxidation–reduction potential, etc., it is reasonable to consider that denitrification mainly occurred in the wetland aquifer through which groundwater flowed. Because the concentration of dissolved N2O was much higher than ambient air, its emission from the water table became the main source of N2O flux in the study area. The temporal and spatial changes of N2O flux were strongly affected by the concentration of dissolved N2O, precipitation and temperature. Finally, the budget of nitrogen in the groundwater was estimated based on the variations of nitrate, the dissolved N2O and the calculated nitrogen gas along the flow path of groundwater where denitrification was available.