Ammonium and nitrate concentrations were analyzed in near-bottom water and pore water collected from ten stations of the intertidal flat of the Changjiang Estuary during April, July, November and February. The magnitudes of the benthic exchange fluxes were determined on the basis of concentration gradients of ammonium and nitrate at the near-bottom water and interstitial water interface in combination with calculations of a modified Fick’s first law. Ammonium fluxes varied from-5.05 to 1.43 μg/(cm 2 ·d) and were greatly regulated by the production of ammonium in surface sediments, while nitrate fluxes ranged from-0.38 to 1.36 μg/(cm 2 ·d) and were dominated by nitrate concentrations in the tidal water. It was found that ammonium was mainly released from sediments into water columns at most of stations whereas nitrate was mostly diffused from overlying waters to intertidal sediments. In total, 823.75 t/a ammonium-N was passed from intertidal sediments to water while about 521.90 t/a nitrate-N was removed from overlying waters to intertidal sediments. This suggests that intertidal sediments had the significant influence on modulating inorganic nitrogen in the tidal water. Ammonium and nitrate concentrations were analyzed in near-bottom water and pore water collected from ten stations of the intertidal flat of the Changjiang Estuary during April, July, November and February. The magnitudes of the benthic exchange fluxes were determined on the basis of concentration gradients of ammonium and nitrate at the near-bottom water and interstitial water interface in combination with calculations of a modified Fick’s first law. Ammonium fluxes varied from-5.05 to 1.43 μg / (cm 2 · d) and were greatly regulated by the production of ammonium in surface sediments, while nitrate fluxes ranged from-0.38 to 1.36 μg / (cm 2 · d) and were dominated by nitrate concentrations in the tidal water. It was found that ammonium was mainly released from sediments into water columns at the most of stations nitrate was mostly diffused from overlying waters to intertidal sediments. In total, 823.75 t / a ammonium-N was passed from intertidal sediments to water while about 521.90 t / a nitrate-N was removed from overlying waters to intertidal sediments. This suggests that intertidal sediments had the significant influence on modulating inorganic nitrogen in the tidal water.