<p>Treatment wetlands are widespread measures to reduce agricultural diffuse pollution. Systems that are often planted with emergent macrophytes such as Typha spp. and Phragmites spp. are efficient to reduce nutrients, particularly nitrogen and phosphorus compounds. While many experiments have been conducted to study the emission of carbon dioxide (CO<sub>2</sub>) and methane (CH<sub>4</sub>), little attention has been paid for the emission of nitrous oxide (N<sub>2</sub>O). Few studies have been shown that usually N<sub>2</sub>O emission from water saturated ecosystems such as wetlands is low to negligible. In V&#228;nda in-stream treatment wetland that was built in 2015 and located in southern Estonia, we carried out first long term N<sub>2</sub>O measurements using floating chambers. The total area of the wetland is roughly .5 ha; 12 boardwalks, each equipped with two sampling spots, were created. Samples were collected biweekly from March 2019 through January 2021. In each sampling campaign water table depth, water and air temperature, O<sub>2</sub> concentration, oxygen reduction potential, pH and electrical conductivity were registered. Water samples for TN, NO<sub>3</sub>-N, NO<sub>2</sub>-N, TOC, TIC and TC were collected from inflow and outflow of the system in each sampling session and the average concentrations were 5.1 mg/L, 3.68 mg/L, <0.1 mg/L, 41.2 mg/L and 28.7, respectively. Our results showed a very high variability of N<sub>2</sub>O emission: the fluxes ranged from -4.5 ug m<sup>-2</sup> h<sup>-1</sup> to 2674.2 ug m<sup>-2</sup> h<sup>-1</sup> with mean emission of 97.3 ug m<sup>-2</sup> h<sup>-1</sup>. Based on gas samples (n=687) we saw a strong correlation (R<sup>2</sup> = -0.38, p<0.0001) between N<sub>2</sub>O emission and water depth. The average N<sub>2</sub>O emission from sections with the water table depth >15 cm was 45.9 ug m<sup>-2</sup> h<sup>-1</sup> while sections with water table depth <15 cm showed average emission of 648.3 ug m<sup>-2</sup> h<sup>-1</sup>. The difference between these areas was more than 10 times. Water temperature that is often considered as the main driver had less effect to the N<sub>2</sub>O emission. For instance, at lower temperatures, when the emissions from deeper zones decreased, there was no temperature effect on emissions from shallow zones. We also saw that over the years the overall N<sub>2</sub>O emission followed clear seasonal dynamics and has a slight trend towards lower emissions. This can be related to the more intensive vegetation growth that has been increased from ~40% in 2019 to approximately 90% in 2020. Our study demonstrates that the design of the wetland is not only important for the water treatment, but it can also determine the magnitude of greenhouse gas emissions. We saw that even slight changes in water table depth can have a significant effect on the annual N<sub>2</sub>O emission. Thus, in-stream treatment wetlands that have water table depth at least 15 cm likely have remarkably lower N<sub>2</sub>O emissions without losing water treatment efficiency.</p><p>&#160;</p>