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Estuaries play a key role in moderating the flow of nitrogen (N) to marine ecosystems. However, the magnitude of this N removal can vary dramatically both within and between estuaries due to the benthic habitats present. Here, we compare denitrification, coupled nitrification–denitrification, anammox, and dissimilatory nitrate reduction to ammonium (DNRA) across a mosaic of benthic habitats in the subtropical Noosa River Estuary, Australia. Using 15N tracer techniques and passive pore‐water samplers, we show that coupled nitrification–denitrification was the dominant pathway for N2 production across all habitats, with higher rates in vegetated habitats (10–70 μmol N m−2 h−1) compared to bare sediments (0.9–2 μmol N m−2 h−1). Unusual pore‐water profiles in the macroalgal sediments suggest the presence of sulfur‐driven anoxic nitrification of NH4+ to NO3− and N2. A benthic N budget showed that combined denitrification and coupled nitrification–denitrification accounted approximately 96% of the N2 production, while DNRA accounted for 9% of total NO3− reduction pathways in the Noosa River Estuary. The macroalgae habitat contributed 76% of total N removal via N2 production and 65% of N retention via DNRA, despite accounting for only 25% of the total surface area. We show a strong relationship between seagrass and macroalgae area and N2 production (r2 = 0.8; p < 0.01), and as such, the capacity to mitigate reactive N loads in estuaries may decrease with the large‐scale loss of seagrass and other vegetated habitats.

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Industrialized agriculture and the burning of fossil fuels have significantly altered the global nitrogen (N) cycle (Galloway, 2014;Rockström et al., 2009). Large amounts of reactive N are now transported from terrestrial to coastal environments via estuaries. Estuaries are important sites of N removal via denitrification (Eyre et al., 2016;Seitzinger et al., 2006), but also produce nitrous oxide (N 2 O) as an intermediate product (Duan et al., 2017). Nitrous oxide is a powerful greenhouse gas with a global warming potential nearly 300 times greater than carbon dioxide over a time period of 100 years (IPCC, 2013). Approximately 57% of N 2 O comes from natural sources (e.g., lightning, soils, and the ocean), while 43% is from anthropogenic activities (e.g., agriculture, industrial activities and fossil fuel combustion) (Tian et al., 2020). Although estuaries represent about 0.4% of the global ocean area, on average they contribute about 10% of the N 2 O emissions of the open ocean (0.31 Tg N yr −1 ), and this could be as high as 100% (−0.005 to 4.8 Tg N yr −1 ) (Murray et al., 2015).Nitrous oxide emissions from estuaries are expected to increase due to anthropogenic N loading (Borges et al., 2018;Turner et al., 2016;Wells et al., 2018). However, most previous estuarine studies have measured N 2 O fluxes across the water-air interface (e.g., Brase et al., 2017;Murray et al., 2015;Wells et al., 2018), which are essentially an integration of the various source inputs and sediment N 2 O cycling. To date, very few studies have