Stable nitrogen isotopes were used to assess the effects of wastewater treatment plant (WWTP) upgrades on the utilisation of sewage-N by estuarine biota in Moreton Bay, Australia. We measured d15N of filamentous algae, mangrove leaves and shore crabs at the Brisbane and Logan Rivers before and after scheduled WWTP upgrades, and at two reference rivers where WWTPs had been upgraded >4 years previously. The total N discharged into Brisbane River decreased by >80% after the upgrades had occurred, but N loads remained similar at Logan River despite the upgrade. In Brisbane River, d15N values of algae and crabs decreased and were comparable to the reference rivers within 1-2 years but no changes occurred at Logan River. The d15N of mangrove leaves remained elevated in all rivers, indicating that sewage-N remained a major source to mangroves either from residual WWTP discharges or from N accumulated in the sediments over many years.