Abstract. The balance between denitrification and nitrogen fixation is the key control of the availability of nitrogen in coastal ecosystems and thus the primary productivity of these environments. However, evaluating the importance of denitrification and nitrogen fixation over large spatial and temporal scales is problematic. In this study, a combined mass and stable isotope balance of nitrogen was used to constrain the cycling of nitrogen in Western Port, Victoria – a temperate, intertidal embayment in south-eastern Australia. This method is a more effective approach compared to the extrapolation of discrete measurements and geochemical approaches. The validity of the isotope and mass balance model has been tested by comparing the output of the model with the average measured isotopic signature of the sediment in Western Port. Using previously measured rates of nitrogen fixation and denitrification in combination with the isotopic signature of nitrogen inputs from the catchment, atmosphere and the marine environment, the model returned an isotopic signature of 4.1 ± 2.5 ‰. This compares favorably with the average measured isotopic signature of the sediment of 3.9 ± 1.2 ‰. Sensitivity analysis confirmed that it was the isotopic values of the end-members, fractionation factors of assimilation and denitrification that exerted the greatest control over the isotopic signature of the sediment and not the loadings of the source and sink terms. Analysis of the relative importance of the various nitrogen inputs into the bay suggests that nitrogen fixation contributes 36 % of the total nitrogen inputs to Western Port.