Greenhouse gas (GHG) mitigation strategies are often constrained by rice farmers’ preferences, therefore an assessment of mitigation strategies taking farmers’ constraints into consideration, are important for their pos- sible adoption. The field experiments were conducted for two continuous rice-growing seasons in northern Vietnam, to evaluate the effectiveness of drainage patterns on methane (CH4) and nitrous oxide (N2O) emissions under farmers’ variable conditions. Two improved drainage practices (pre-planting plus midseason [PM] drai- nage and early-season plus midseason [EM] drainage) were compared with local practices of water management (midseason drainage [M] and conventional continuous flooding (control) [C]) with full residue [F] and reduced residue [R] (local practice of residue management) incorporation. The GHG mitigation potential of water re- gimes was tested in two water management systems (efficient field water management [EWM] system and inefficient field water management [IWM] system). In EWM system, EM resulted an average 14% and 55% reduction in CH4 emissions compared to M with R and F respectively. The EM lowered the CH4 emissions by 67% and 43% compared to C in the EWM and IWM respectively. The EM and PM resulted in higher N2O emissions compared to M (25–36%) and C (42–43%) in both systems. The contribution of increased N2O emissions with EM and PM to global warming potential (GWP) was negligible. EM reduced the GWP by 42% compared to C with F in the IWM system, and by 20–52%, 30–62% and 66% compared to M, PM and C respectively in the EWM system. Furthermore, greenhouse gas intensity (GHGI) reduced by 22–72% in the EWM than in IWM. This study demonstrates that efficient field water management system has a positive impact on over-all GHG mitigation potential of drainage practices in farmers’ field conditions.