Lowland rice cultivation is a major contributor to agricultural greenhouse gas (GHG) emissions. Managing water and fertilizer is important GHG emissions. This paper evaluated GHG emissions of rice production under contrasting water regimes, i.e., continuous flooding (CF) versus alternate wetting and drying (AWD), with six nitrogen fertilizer combinations: no nitrogen (F1), urea 175 kg ha-1 (F2), urea 350 kg ha-1 (F3), urea 262.5 kg ha⁻¹ + manure 3 tons ha-1 (F4), urea 525 kg ha⁻¹ + rice straw 3 tons ha-1 (F5), and urea 175 kg ha⁻¹ + manure 3 tons ha-1 + biochar 0.6 tons ha-1 (F6). The field experiments were conducted at Bogor Regency, West Java, Indonesia, using a randomized complete block design with three replications. Growth, yield components, and GHG emissions were observed in this study throughout the growing season. Results showed AWD reduced CH₄ emissions by 30% but increased N₂O by 43% compared to CF, yielding a net 23% lower global warming potential (GWP). Organic-amended treatments (F6) maintained yields equivalent to conventional fertilization while showing numerically lower GWP. The independent effect of the water regime and the nitrogen fertilizer combinations implies that the best level of biochar and manure combined with AWD has the most promising prospect of maintaining rice yield while reducing GHG emissions.