Water resource recovery facilities (WRRFs) contribute to climate change and air pollution, as they are anthropogenic potential sources of direct and indirect emission of greenhouse gases (GHGs). Studies concerning the monitoring and accounting for GHG emissions from WRRFs are of increasing interest. In this study, the floating hood technique for gas collection was coupled with the off-gas method to monitor and apportion nitrous oxide (N2O) and carbon dioxide (CO2) emissions from both aerated and non-aerated tanks in a municipal water resource recovery facility, in order to investigate its carbon footprint (CFP). To our knowledge, this is the first time that the chamber technique was applied to evaluate gas fluxes from the settler, where an emission factor (EF) of 4.71 ∗ 10-5 kgCO2,eq kgbCOD-1 was found. Interesting results were found in the disinfection unit, which was the major contributor to direct N2O emissions (with a specific emission factor of 0.008 kgCO2,eq kgbCOD-1), due to the chemical interaction between hydroxylamine and the disinfectant agent (hypochlorite). The specific emission factor of the biological aerated tank was 0.00112 kgCO2,eq kgbCOD-1. The average direct CO2 emission was equal to 0.068 kgCO2 kgbCOD-1 from the activated sludge tank and to 0.00017 kgCO2 kgbCOD-1 from the secondary clarifier. Therefore, taking into account the contribution of both direct N2O and CO2 emissions, values of 0.069 kgCO2,eq kgbCOD-1, 0.008 kgCO2,eq kgbCOD-1 and 0.00022 kgCO2,eq kgbCOD-1, were found for the net CFP of the aerated compartment, the disinfection unit and the clarifier, respectively. The plant energy Footprint (eFP) was also evaluated, confirming that the aeration system is the major contributor to energy consumption, as well as to indirect CO2 emission, with a specific eFP of 1.49 kWh kgbCOD-1.