Microalgae can synthesise the ozone depleting pollutant and greenhouse gas nitrous oxide (N2O). Consequently, significant N2O emissions have been recorded during real wastewater treatment in high rate algal ponds (HRAPs). While data scarcity and variability prevent meaningful assessment, the magnitude reported (0.13–0.57% of the influent nitrogen load) is within the range reported by the Intergovernmental Panel on Climate Change (IPCC) for direct N2O emissions during centralised aerobic wastewater treatment (0.016–4.5% of the influent nitrogen load). Critically, the ability of microalgae to synthesise N2O challenges the IPCC's broad view that bacterial denitrification and nitrification are the only major cause of N2O emissions from wastewater plants and aquatic environments receiving nitrogen from wastewater effluents. Significant N2O emissions have indeed been repeatedly detected from eutrophic water bodies and wastewater discharge contributes to eutrophication via the release of nitrogen and phosphorus. Considering the complex interplays between nitrogen and phosphorus supply, microalgal growth, and microalgal N2O synthesis, further research must urgently seek to better quantify N2O emissions from microalgae-based wastewater systems and eutrophic ecosystems receiving wastewater. This future research will ultimately improve the prediction of N2O emissions from wastewater treatment in national inventories and may therefore affect the prioritisation of mitigation strategies.