The emissions of nitrous oxide (N2O) and nitric oxide (NO) from biological nitrogen removal (BNR) operations via nitrification and denitrification is gaining increased prominence. While many factors relevant to the operation of denitrifying reactors can influence N2O and NO emissions from them, the role of different organic carbon sources on these emissions has not been systematically addressed or interpreted. The overall goal of this study was to evaluate the impact of three factors, organic carbon limitation, nitrite concentrations, and dissolved oxygen concentrations on gaseous N2O and NO emissions from two sequencing batch reactors (SBRs), operated, respectively, with methanol and ethanol as electron donors. During undisturbed ultimate-state operation, emissions of both N2O and NO from either reactor were minimal and in the range of <0.2% of influent nitrate-N load. Subsequently, the two reactors were challenged with transient organic carbon limitation and nitrite pulses, both of which had little impact on N2O or NO emissions for either electron donor. In contrast, transient exposure to oxygen led to increased production of N2O (up to 7.1% of influent nitrate-N load) from ethanol grown cultures, owing to their higher kinetics and potentially lower susceptibility to oxygen inhibition. A similar increase in N2O production was not observed from methanol grown cultures. These results suggest that for dissolved oxygen, but not for carbon limitation or nitrite exposure, N2O emission from heterotrophic denitrification reactors can vary as a function of the electron donor used. Biotechnol. Bioeng. 2010; 106: 390–398. © 2010 Wiley Periodicals, Inc.