The Yarra River estuary is a salt-wedge estuary prone to periods of stratification-induced anoxia and hypoxia (O-2 <100 mu mol L-1) during low-flow events. Nitrate reduction pathways were examined using the N-15 isotope pairing technique in intact sediment cores, emulating in situ conditions, to evaluate the fate of NO3- during changing oxygen conditions. Water-column concentrations of dissolved inorganic carbon (DIC), O-2, NH4+, and NOx (NO3- + NO2-) were also measured to examine any deviation from conservative behavior (denoted Delta) in response to oxygen variability within the estuary. The estuary was a source of NH4+ in the anoxic bottom waters. Whole-system estimates using deviations from conservative behavior and core incubations were in good agreement and showed that NH4+ was regenerated more efficiently relative to DIC under hypoxic conditions. For the whole system, mean Delta DIC : Delta NH4+ ratios under oxic (85 +/- 33) and hypoxic (20 +/- 3) conditions were significantly different. The more-efficient NH4+ regeneration during hypoxia was attributed to rapid mineralization rates and cessation of nitrification; dissimilatory nitrate reduction to ammonium (DNRA) was not a significant contributor. Unexpectedly, the denitrification : DNRA ratio was significantly higher under hypoxic conditions, with denitrification contributing 99.1 +/- 0.3 of total nitrate reduction. DNRA rates were significantly higher during oxic conditions (123.5 +/- 30.7 mu mol m(-2) h(-1)) when compared with rates during hypoxia (0.6 +/- 0.1 mu mol m(-2) h(-1)). The increase in DNRA in the presence of oxygen was attributed to the alleviation of NO3- limitation during these conditions.