Optimization of land-use practices of rice cultivation for the mitigation of the most significant greenhouse gas (GHG) emissions from agriculture methane (CH4) and nitrous oxide (N2O) is challenging and requires confirmation from field studies. In northern Vietnam, we investigated the effects of water and rice residue management on GHG emissions and yields of rice. We used a 2 × 4 factorial design, comparing alternate wetting and drying (AWD) and conventional continuous flooding (Flood) water management, each with four different rice residue treatments: composted residues (compost), on-site burning (ash), plowing residues under (plow), and a control with removal of residues (CT). All plots received equal amounts of NPK fertilizer application. Water management was a major factor in reducing CH4 emissions. AWD management led to a reduction of CH4 emissions by 15−42% under the compost treatment, by 27−47% under ash, and by 36−45% under the plow treatment. Similarly, AWD management resulted in a reduction of the global warming potential (GWP) by 16−36% (CT), 15−39% (compost), 27−40% (ash), and 35−40% (plow), respectively. The latter led to the highest CH4 emissions, while the control (CT) showed the lowest CH4 emissions under both water management systems. Significantly higher N2O emissions were observed for all treatments under AWD water management compared to the respective treatments under flood management. This was especially pronounced after fertilization events. In conclusion, we recommend a combination of plowing under rice residues and AWD water management, as this combination resulted in reduced GHG emissions and lower GWP while ensuring high rice yields.