Denitrification is an important process mitigating nitrogen (N) pollution in aquatic systems. Water samples in 13 sites throughout the Jiulong River Estuary were collected in July, 2010 in a preliminary investigation of the denitrification rate in this area. As end-products of denitrification, dissolved N2 was measured by determining N2 : Ar ratios using MIMS (HPR-40), while the concentration of nitrous oxide (N2O) dissolved in water was determined by Purge and Trap-Gas Chromatography. The results showed significant spatial variance of net increase of dissolved N2 (ranging between - 9.9 and 66.8 micromol x L(-1)) and N2O (ranging between 4.3 and 31.5 nmol x L(-1)) in the Jiulong River Estuary. The net increase of dissolved N2 and N2O declined gradually from river sites to sea sites. Dissolved N2O was supersaturated by 170%-562%. The air-water fluxes of N2 ranged between -2.9 and 53.2 mmol x (m2 x d) (-1), and N2O between 5.2 and 23.9 micromol x (m2 x d)(-1). The N2O yield shared only 0.03% - 1.2% (average 0.25%) of total N air-water flux. The results suggested that water temperature and nutrient (N and P) were the key factors influencing denitrification. The denitrification rate is controlled by nitrate level at fresh-water sites with salinity < 0.5%. However, in salty waters, net increase in N2 and N2O mainly originated from denitrification occurring upstream of the estuary, and was dominated by the salinity gradient due to tidal mixing.