N2 flux rates (net denitrification) were measured over a diel cycle, seasonally, in 12 benthic habitats across three warm temperate Australian coastal systems. Dark N2-N fluxes were strongly controlled by sediment oxygen demand (SOD) across the 3 estuaries, 4 seasons, and 12 benthic habitats (r2 = 0.743; p < 0.001; n = 142; slope = 0.0170). However, some of the slopes differed significantly between seasons and among estuaries and habitats, and all of the slopes were correlated with the δ13C values and C:N ratios of sediment organic matter. Ternary mixing diagrams with the contribution of algal, seagrass, and terrestrial/mangrove material to sediment organic matter showed that habitats, seasons, and estuaries dominated by a mixture of seagrass and algal material had the lowest slopes, and slopes increase as habitats, seasons, and estuaries have an increasing contribution from terrestrial/ mangrove material. Overall, the slopes of dark N2 fluxes versus SOD were low compared to previous studies, most likely due to either, or a combination of, the C:N ratio of the organic matter, the mixture of C:N ratios making up the organic matter, the structure of the organic matter, and/or the SOD rates. This study demonstrated that it is not only the quantity but also the type (quality), and maybe the mixture, of organic matter that is an important control on denitrification. As such, rapid global changes to detrital sources to coastal systems due to losses of mangrove, seagrasses, and saltmarshes, and associated increases in algae and macrophytes, are also expected to impact system level losses of nitrogen via denitrification.