Global agriculture faces the challenge of meeting food demand while minimising environmental impacts such as greenhouse gas (GHG) emissions. The maize-wheat cropping system, vital for food security in South and East Asia, traditionally involves intensive fertiliser use and flood irrigation that exacerbate GHG emissions and degrade soil health. This study evaluated the effectiveness of integrated nutrient management (INM), organic, natural, and chemical nutrient practices combined with surface and subsurface drip irrigation on GHG emissions, crop productivity, and economic returns. Results demonstrated that INM coupled with drip irrigation significantly reduced CO₂ and N₂O emissions while improving nutrient use efficiency and maximising yields. Economic analysis indicated that INM and natural farming treatments maintained higher benefit-cost ratios (up to 1.59) and lower total annual costs (as low as ₹85,057) compared to organic and chemical treatments. Although chemical fertilisation resulted in higher incomes, it incurred elevated emission costs, reflecting negative externalities that reduce sustainability. The findings support the adoption of integrated nutrient and water management strategies for the sustainable intensification of maize-wheat systems, balancing productivity, profitability, and environmental stewardship. The study faced challenges related to the accurate quantification of GHG fluxes under field conditions, high initial investment costs of drip systems, and site-specific variability in soil–climate interactions. Despite these constraints, this work contributes robust field-based evidence on the energy–water–carbon nexus and provides a scalable framework for integrating drip irrigation with climate-smart nutrient management for sustainable intensification of maize–wheat systems.