Mitigation of greenhouse gases (GHGs), improving nutrient-use efficiency (NUE), and maximizing yield in rainfed lowland rice cultivation poses significant challenges. To address this, a two-year field experiment (2020 and 2021) was conducted in Assam, India, to examine the impact of different fertilizer-management practices on grain yield, NUE, and GHGs in wet direct-seeded rice (Wet-DSR) during the kharif season. The experiment included eight treatments: control; farmer’s practice (30-18.4-36 kg N-P₂O₅-K₂O ha⁻¹); state recommended dose of fertilizer (RDF) @ 60-20-40 kg N-P₂O₅-K₂O ha⁻¹ with N applied in three splits @ 30-15-15 kg ha⁻¹ as basal, at active tillering (AT), and panicle initiation (PI); best fertilizer management practices (BMPs): 60-20-40 kg N-P₂O₅-K₂O ha⁻¹ with N applied in three equal splits as basal, at AT, and PI; and fertilizer deep placement (FDP) of 120%, 100%, 80%, and 60% N combined with 100% PK of RDF. The experiment was arranged out in a randomized complete block design with three replications for each treatment. The highest grain yield (4933 kg ha⁻¹) and straw yield (6520 kg ha⁻¹) were achieved with the deep placement of 120% N + 100% PK of RDF. FDP with 80% N + 100% PK reduced 38% N₂O emissions compared to AAU’s RDF and BMPs, where fertilizer was broadcasted. This is mainly due to the lower dose of nitrogen fertilizer and the application of fertilizer in a reduced zone of soil. When considering both productivity and environmental impact, applying 80% N with 100% PK through FDP was identified as the most effective practice.