A wetland is an important part of the headwater in the discharge area of a basin. It controls not only groundwater discharge such as seepage or springs, but also the migration of chemical matter from the basin. In order to make clear how and where natural attenuation processes happen in wetlands, a typical headwater in Chiba, Japan, was chosen for an investigation of the behaviour of nitrate in groundwater. From the viewpoint of hydro-geomorphology, the wetland in the study site can be divided into three zones: the shallow water-table zone, the seepage zone, and the spring zone along the downstream direction. There were six piezometer groups; each group contained four piezometers, individually set at depths of 1, 2, 3 and 4 m. Major ions and 15N of groundwater from piezometers, wells and springs were analysed. It was found that nitrate in groundwater mainly came from the fertilizers used in the upstream recharge area of the study site. When the groundwater moved up across the wetland, nitrate concentration in the groundwater decreased rapidly in the shallow water-table zone due to denitrification. Nitrate-free water can be found at the seepage zone. However, the behaviour of nitrate in the spring water was different from that in the seepage zone, since both dilution and denitrification processes were involved in the decrease of nitrate concentration in groundwater. In particular, the dilution process mainly controlled the decline of nitrate at the location where the nitrate-free groundwater flowing horizontally from the seepage zone mixed with the high-nitrate groundwater flowing upward before emerging as a spring. It was also found that denitrification only occurs suddenly in a narrow zone or a thin layer of the order of a few metres.