As the need for sustainable rice cultivation increases, irrigation with treated sewage effluent (TSE) has become a reasonable solution and its impact on the emission of greenhouse gas (GHG), CH 4 and N 2 O, has gained increasing attention. Despite TSE containing dissolved GHGs, previous studies have not focused on the spatiotemporal profile and impact of TSEs on GHG assessments. Therefore, we conducted an experiment with the pilot-scale reactor using TSE irrigation to assess the importance of the dissolved GHG profiles. The TSE originally contained dissolved CH 4 and N 2 O. The results showed that the dissolved CH 4 concentrations in the TSE were higher than those in the paddy fields. Although the TSE contained dissolved N 2 O, it was also produced in the soils. Moreover, microorganisms, such as Candidatus Nitrotoga arctica and Methanospirillum, became dominant species. Our study demonstrates that measuring the spatiotemporal profiles of dissolved GHGs in paddy fields, as well as in TSE, can lead to more reliable GHG monitoring by assessing the dissolved GHGs in the inflow and outflow of paddy fields.