The large global warming potential of nitrous oxide (N2O) is currently of general concern for the water industry, especially in view of a new regulatory framework concerning the carbon footprint of water resource recovery facilities (WRRFs). N2O can be generated through different biological pathways and from different treatment steps of a WRRF. The use of generic emission factors (EF) for quantifying the emissions of WRRFs is discouraged. This is due to the number of different factors that can affect how much, when and where N2O is emitted from WRRFs. The spatial and temporal variability of three WRRFs in Europe using comparable technologies is presented. An economically feasible and user-friendly method for accounting for the contribution of anoxic zones via direct gas emission measurements was proven. The investigation provided new insights into the contribution from the anoxic zones versus the aerobic zones of biological WRRF tanks and proved the unsuitability of the use of a single EF for the three WRRFs. Dedicated campaigns for N2O emissions assessment are to be advised. However, similarities in the EF magnitude can be found considering treatment strategy and influent water composition.