Diazotrophic cyanobacteria are capable of fixing atmospheric N2 to satisfy their physiological nitrogen requirements. This process can result in the transfer of substantial amounts of "new" diazotrophic nitrogen (ND) to aquatic ecosystems during blooms of these taxa. Using in situ measurements of plankton natural abundance stable isotope composition and a combination of underway and fixed site survey data, the total N(D) flux into the Gippsland Lakes estuary (Australia) was estimated during a summer bloom of the diazotrophic cyanobacterium Nodularia spumigena. Over the course of the bloom, N(D) increased in the upper water column of the estuary from 33% +/- 17% (mean +/- SD) to 73% +/- 13% of the standing pool of total particulate N. A conservative estimate of total N(D) flux (146 Mg) equates to an estimated 177% of the summer total N load and 22% of the annual total N load to the estuary. Combining natural abundance stable isotope measurements with relatively simple fixed and underway survey designs can provide a cost-effective approach for monitoring the N(D) flux into estuary or lacustrine environments. This approach relies on an isotopic differential between the diazotrophic and the non-diazotrophic components of the plankton community; it may not be appropriate in ecosystems that experience low-level blooms or blooms of intermittent N-fixing cyanobacteria. Large-scale blooms of diazotrophic cyanobacteria are considered uncommon in estuaries, yet it is clear that these blooms can represent major sources of new N to estuarine ecosystems when and where they occur.