Population growth and urbanization are driving the demand for centralized wastewater treatment, a primary source of N₂O and CH₄ emissions. We have conducted the first comprehensive assessment of CH₄, N₂O and NH₃ emissions across diurnal, day-to-day and seasonal scales at 96 US water resource recovery facilities (WRRFs) that collectively treat 9% of US centralized wastewater. Facility-level emissions were scaled to the national level using a probabilistic approach. Here we show that the measured emissions were 1.9 times higher for N₂O (95% confidence interval (CI): 1.3–2.6) and 2.4 times higher for CH₄ (CI: 1.9–2.9) than current US inventories. Considering the cumulative climate impacts of CH₄ and N₂O, the top 10% of emitters contributed 74% of the carbon footprint, with the top half contributing 98%, highlighting priorities for mitigation. Although detected at only a small fraction of facilities, measurements of NH₃ emissions (86 kt yr⁻¹ in the USA) suggest WRRFs are an overlooked source of urban NH₃. Finally, the contribution of centralized wastewater treatment to global greenhouse gas emissions will increase 2- to 17-fold by 2100 under future scenarios. Overall, greater consideration of wastewater treatment emissions is needed to reach sustainability targets.