Flooded organic soils are potentially important sources of greenhouse gases. The effect of soil temperature and moisture on the concentration of N₂O and CO₂ at two depths of organic soil flooded with two doses of purified wastewater was studied. Nitrous oxide concentrations at the 10-30 cm depth range were generally increased with an increase in soil moisture, showing dependence on the aeration status of soil. The maximum values of N₂O concentrations were higher at the 50-100 than 10-30 cm depth range, but a similar pattern of increasing maximum values of N₂O concentration with an increasing input of nitrogen in treatments at both depth ranges was observed. The maximum concentrations of carbon dioxide within the 50-100 cm depth range remained at a similar level in all treatments reaching 7.1-7.7%, which indicated weak relations with the input of water and nitrogen at this depth range. We conclude that the N₂O and CO₂ concentrations at 10-30 cm depths in the examined organic soil flooded with 600mm year-1 of purified wastewater exhibited a similar level as the concentrations in soil watered only by precipitation.