Emissions of greenhouse gases (GHG) from paddy rice are significant, so reducing these emissions has significant potential for climate change mitigation. We investigated alternate wetting and drying (AWD) as part of an integrated management approach to enhance mitigation, together with combinations of mineral nitrogen (N), reduced tillage, a suitable combination of plant residues and well decomposed manure. To quantify GHG emissions, and the potential for mitigation without yield decline, a process-based model, DayCent was used to simulate methane (CH4) and nitrous oxide (N2O) emissions from paddy rice (Oryza sativa L.) in Bangladesh. The four test sites selected were amended with mineral N fertilizer or an organic amendment (rice straw). A good agreement (p < 0.05) was observed between model simulated and measured daily CH4 flux at most of these test sites with no significant bias. The seasonal CH4 emission from a site receiving mineral N fertilizer at a rate of 110 kg N ha(-1) was predicted by the model to be 210 and 150 kg ha(-1) for the water management scenarios of continuous flood (CF) and AWD, respectively. These values compare well with estimates of CH4 emissions using Intergovernmental Panel on Climate Change tier 1 methods for the different water regimes. Our model results suggest emission factors for N2O of 0.4% and 0.6% of applied fertilizer under CF and AWD water regimes, respectively. Based on modelling studies, AWD was found to be an important strategy not only with respect to reducing GHG emissions, but also in terms of cost effectiveness. We also found that integrated management is a promising option for farmers and policy makers interested in either yield increase, GHG mitigation or both. Yield scaled emissions intensity under AWD was found to be about 24% lower than under CF, followed by integrated management.