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.