Mangrove forests can be a source or a sink of nitrous oxide (N2O) to the atmosphere, but seasonal mangrove N2O dynamics are not well understood. We used continuous high-resolution N2O concentration data to construct seasonal budgets of N2O in two tropical mangrove-lined creeks for both the wet and dry seasons. Furthermore we used N stable isotope analysis to constrain the pathways of N2O production and consumption within these creeks. Calculated water-air fluxes were within a range typical of undisturbed mangroves, however obvious seasonal differences in N2O dynamics were observed at the two sites. The mangrove systems were a net source of N2O to the atmosphere during the dry season and a net sink during the wet season. In the wet season we propose that increased allochthonous carbon enhances N2O consumption by denitrification. Combining the seasonal fluxes, the Fitzroy mangrove system, which received a continual input of allochthonous nitrate (NO3−), was a net source of N2O, while the Burdekin mangrove system was close to a net N2O balance. Interpreted in the context of DIN and N2O concentrations, the N2O isotopic values observed in the dry season point to fungal denitrification as the most likely pathway of N2O production. This study shows that subtle shifts in seasonal nutrient supply regulate mangrove N2O production and consumption.