In dry season paddy farming, the alternate wetting and drying (AWD) irrigation improves water productivity, paddy production, and has the potential to decrease greenhouse gas (GHG) such as methane (CH4) and nitrous oxide (N2O) emissions when compared to continuous flooding (CF). However, there is a lack of research in Bangladesh on the effects of water management on CH4 and N2O emissions. During November 2017–April 2018, participatory on-farm trials were conducted at Feni and Chattogram districts of Bangladesh. Total 105 farmers comprising 20-hectare of land (62 farmers at Feni and 43 farmers at Chattogram district, each location having 10 hectare of land). We compared irrigation water and cost reductions, paddy yield, and CH4 and N2O emissions from paddy fields irrigated using AWD and CF irrigation methods. The CH4 and N2O emissions were determined using the Cool Farm Beta-3 methodology, and the global warming potential (GWP) was estimated using the Intergovernmental Panel on Climate Change-2014 standard approach. The mean results of randomly selected 30 farmers from two locations (15 of each) showed that AWD remarkably decreased irrigation water consumption by about 24% and increased water productivity by 224%. We estimated 23% savings for irrigation costs in AWD. By this time, AWD improved paddy production by 3% over CF. The AWD irrigation resulted in a 47% reduction in cumulative CH4 emissions having a lower CH4 emission factor (0.74 kg ha-1 day-1) than CF (1.39 kg ha-1 day-1). There was no obvious difference in N2O emission between AWD and CF. When compared to CF, AWD decreased the overall GWP by 27% and lowered the GHG intensity by 42%. The CH4 and N2O emissions did not differ substantially between Feni and Chattogram.