Intertidal wetlands can sequester pollutants along estuarine conduits. Here we test the effectiveness of a mangrove-dominated estuary in removing dissolved nitrogen during a rain event. We intensively and simultaneously sampled surface water nutrients upstream and downstream of an estuary before, during and after a 63 mm rain event in Coffs Creek (Australia). NO was the main form of dissolved nitrogen upstream of the estuary (∼60%), while dissolved organic nitrogen (DON) was an important form at the downstream station (∼46%) during observations. High NO attenuation (71%) occurred during the rain event when the loads reached 31 μmol m catchment area day. In contrast, the estuary was found to be a source of NH (∼5 μmol m catchment area day). This implies a moderate conversion of upstream NO into NH and DON along the transport pathway, likely due to tidally-driven pore water exchange within the anoxic estuarine mangrove sediments. Overall, the mangrove-lined estuary attenuated upstream total dissolved nitrogen loads, maintaining water quality and minimizing exports to the coastal ocean even during high flow conditions.