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The increase of salt concentrations in influent wastewaters will be a consequence of the sea level rises in coastal areas due to climate change and the future use of seawater to flush toilets as a cost-attractive option for alternative water resources. Yet, little is known about the salinity effect on full-scale wastewater treatment plants (WWTPs) performance and on greenhouse gas (GHG) emissions, such as nitrous oxide (N2O). This study aimed at quantifying the N2O emissions of a full-scale biological aerated filter (BAF) and to correlate the dynamic behavior of the emissions with the process conditions and the periods of infiltration of seawater. A full-scale BAF was monitored for 3 months to assess both their gaseous and liquid N2O fluxes. The total average daily N2O emissions of the plant were 6.16 g N-N2O/kg of NH4-N removed. For the first time at full-scale, a correlation between the N2O emissions and the wastewater influent conductivity (salinity) was found, in which the increase in seawater infiltration in the sewer at high tide augments the daily N2O production and emission to 13.78 g N-N2O/kg of NH4-N removed. The proportional increase in influent conductivity and the N2O emission factor in this WWTP suggested that periods of high conductivity could serve as an indicator of increased N2O emissions by the plant. Furthermore, the operational conditions and the wastewater influent characteristics that influence the N2O emissions were identified as being the dissolved oxygen (DO) dynamics due to the filter washing steps, leading to rapid transitions from oxic to sub-oxic conditions, as well as the (re-)adaptation of microbial consortia due to the dynamics of the biofilm thickness associated to the daily washing process. This study shows the impact that the washing process and seawater infiltration has on the N2O emissions of a BAF and contributes to a better understanding of the operational conditions impacting the emissions in WWTPs.