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Cyanobacterial mats cover extensive areas of subtropical arid coastal wetlands and are sites of active nutrient exchange. To assess spatial (low v. high in the intertidal zone) and temporal (day v. night) variability in nitrogen (N) exchange in arid Exmouth Gulf, Western Australia, we measured nutrient exchange (NOx- -N, NH4+ and soluble reactive phosphorus) during tidal inundation and N fixation of cyanobacterial mats before and during an unusual period of heavy rainfall. Additionally, we investigated the species composition within the cyanobacterial mat. We hypothesised that nutrients are released to the floodwater during tidal inundation, that N fixation is a significant path of N incorporation, that highest N fixation rates occur in the low intertidal zone at night, and that the cyanobacterial mat community composition varies across the intertidal zone. Our results showed that nutrients were removed from the floodwater during tidal inundation. N fixation accounted for 34% of N incorporation, with highest rates in the lower intertidal zone during the day. The cyanobacterial mat was dominated by Microcoleus chthonoplastes, but composition varied across the intertidal zone. The present study provided evidence of temporal and spatial variability in nutrient exchange and implied an important role of cyanobacterial mats in coastal production.