The sustainability of conventional rice (Oryza sativa L.) production systems is often questioned due to the over-mining of groundwater and environmental degradation. This has led to the development of cost-effective, resource-efficient, and environmentally clean rice production systems by optimizing water and nitrogen (N) use. Hence, a 2-year field study (2019 and 2020) was conducted at the ICAR–Indian Agricultural Research Institute, New Delhi, to assess the effect of precision N and water management strategies on growth, land, and water productivity, as well as energy-use efficiency in scented direct-seeded rice (DSR). Two crop establishment methods, conventional-till DSR (CT-DSR) and zero-till DSR (ZT-DSR) along with three irrigation scenarios (assured irrigation (irrigation after 72 h of the drying of surface water), irrigation at 20% depletion of available soil moisture (DASM), and 40% DASM+Si (80 kg ha−1)) were assigned to the main plots; three N management options, a 100% recommended dose of N (RDN): 150 kg ha−1; Nutrient Expert® (NE®)+leaf color chart (LCC) and NE®+soil plant analysis development (SPAD) meter-based N management were allocated to sub-plots in a three-time replicated split-plot design. The CT-DSR produced 1.4, 11.8, and 89.4, and 2.4, 18.8, and 152.8% more grain yields, net returns, and net energy in 2019 and 2020, respectively, over ZT-DSR. However, ZT-DSR recorded 8.3 and 10.7% higher water productivity (WP) than CT-DSR. Assured irrigation resulted in 10.6, 16.1 16.9, and 8.1 and 12.3, 21.8 20.6, and 6.7% higher grain yields, net returns, net energy, and WP in 2019 and 2020, respectively, over irrigation at 20% DASM. Further, NE®+SPAD meter-based N management saved 27.1% N and recorded 9.6, 18.3, 16.8, and 8.3, and 8.8, 21.7, 19.9, and 10.7% greater grain yields, net returns, net energy, and WP over RDN in 2019 and 2020, respectively. Thus, the study suggested that the NE®+SPAD-based N application is beneficial over RDN for productivity, resource-use efficiency, and N-saving (~32 kg ha−1) both in CA-based and conventionally cultivated DSR. This study also suggests irrigating DSR after 72 h of the drying of surface water; however, under obviously limited water supplies, irrigation can be delayed until 20% DASM, thus saving two irrigations, which can be diverted to additional DSR areas.