In this study, methane (CH4) and nitrous oxide (N2O) emission dynamics of a plug–flow bioreactor located in a municipal full-scale wastewater treatment plant were monitored during a period of 10 weeks. In general, CH4 and N2O gas emissions from the bioreactor accounted for 0.016% of the influent chemical oxygen demand (COD) and 0.116% of the influent total Kjeldahl nitrogen (TKN) respectively. In order to identify the emission patterns in the different zones, the bioreactor was divided in six different sampling sites and the gas collection hood was placed for a period of 2–3 days in each of these sites. This sampling strategy also allowed the identification of different process perturbations leading to CH4 or N2O peak emissions. CH4emissions mainly occurred in the first aerated site, and were mostly related with the influent and reject wastewater flows entering the bioreactor. On the other hand, N2O emissions were given along all the aerated parts of the bioreactor and were strongly dependant on the occurrence of process disturbances such as periods of no aeration or nitrification instability. Dissolved CH4 and N2O concentrations were monitored in the bioreactor and in other parts of the plant, as a contribution for the better understanding of the transport of these greenhouse gases across the different stages of the treatment system.