Abstract Alternate wetting and drying (AWD) water management is being promoted to replace continuous flooding (CF) water regime in rice cultivation for agricultural countries, including Thailand, to achieve the net zero greenhouse gas (GHG) emissions and cope with drought. However, its adoption in different areas yielding variable results that requires the careful approaches to prevent negative impacts on rice yield, particularly the aroma of fragrant rice, along with mitigating GHG emissions, mainly methane (CH4) and nitrous oxide (N2O). This study aims to assess the impacts of AWD on CH4 and N2O emissions, productivity, water use, and soil characteristics of fragrant rice cultivation in Thailand. Khao Dawk Mali (KDML) 105 cultivar was cultivated in the wet season and Pathum Thani (PTT) 1 cultivar was planted in the dry season under CF and AWD at different dry levels of 10 cm (AWD10), 15 cm (AWD15), and 20 cm (AWD20) below the soil surface. The emissions of GHG and water use were measured throughout the study period using closed-chamber technique and water meter equipment, respectively. Rice yields and soil properties were analyzed after crop harvesting. The results showed that rice cultivation under AWD in both wet and dry seasons reduced CH4 emissions (18.4%–27.6%) but stimulated N2O emissions (11.8%–15.0%). However, its global warming potential (GWP) was lower than CF, lowered by an average of 17.7%, 26.8%, and 25.5% under the AWD10, AWD15, and AWD20, respectively. Relative to CF, unsuccessful AWD in the wet season did not change rice yield quantity and aroma (2-acetyl-1-pyrroline: 2AP) of KDML 105. Conversely, successful AWD10 and AWD15 in the dry season promoted rice grain yield and 2AP (0.27–0.33 ppm) of PTT1, while AWD20 did not alter rice yield amount but increased rice aroma (0.47 ppm). AWD can save irrigation water in the range of 12.8%–23.0% and 15.5%–18.7% in the wet and dry seasons, respectively. AWD water regime did not importantly change the soil characteristics after crop harvest. This study concludes that AWD, especially AWD15 and AWD20, has the potential to reduce GHG emissions without affecting the quantity and quality of rice yield, along with saving water.