Nitrous oxide (N₂O) is an important greenhouse gas. However, N₂O emissions from estuaries underlie significant uncertainties due to limited data availability and high spatiotemporal variability. We found the Elbe Estuary (Germany) to be a year-round source of N₂O, with the highest emissions in winter along with high nitrogen loads. However, in spring and summer, N₂O emissions did not decrease alongside lower nitrogen loads because organic matter fueled in situ N₂O production along the estuary.