Puddled transplanted rice (Oryza sativa L.) followed by intensively tilled wheat (Triticum aestivum L.) (R–W) is the most predominant cropping system and the lifeline for billions of people in South Asia. The cultivation of R–W system requires high amounts of water, nutrients and energy, resulting in increased production costs and increased emissions of greenhouse gases. There are also increasing concerns of yield stagnation or decline in the R–W system, with increasing environmental footprints. Hence, the sustainability of the R–W system in South Asia, particularly in the northwest Indo-Gangetic Plains (IGPs), has been questioned and heavily debated. Based on the findings from peer-reviewed literature, this review aims to identify unsustainability issues and research gaps in the R–W system and propose possible solutions to mitigate those issues and technological interventions to close the research gaps. Among the unsustainability issues that the review has identified are declining crop, water and land productivity, deterioration of soil health, emissions of greenhouse gases due to intensive tillage and residue burning, deepening of groundwater levels and shift in weed flora and development of herbicidal resistance in crops. Potential solutions or technological interventions to mitigate the unsustainability issues include resource conservation technologies (RCTs) such as rice residue management, reduced tillage, laser land leveling, soil matric potential based irrigation scheduling, delayed rice transplanting, cultivation on permanent raised beds, direct-seeded rice (DSR), mechanical transplanting of rice and crop diversification with legumes. These interventions have the potential to reduce energy, water and carbon (C) footprints from the R–W system. Rice residue retention with Happy Seeder and adoption of zero tillage (ZT) for wheat establishment have significantly lowered the environmental footprints, with increased soil C sequestration due to additions of large amounts of plant-mediated C input. Residue mulching has helped increase root length of wheat by ~25% and root length density by ~40% below 15 cm depth, compared to no mulching. The Happy Seeder saved ~30% of irrigation water due to reduction of soil evaporation by ~42–48 mm through residue mulching. Crop cultivation on permanent raised beds is less energy-intensive and results in ~7.8–22.7% higher water use efficiency yet crop productivity in long run could be affected due to reduced root growth on beds. The puddled transplanted rice (PTR) established under wet tillage, however, can decrease the water percolation losses by 14–16% and crop water demand by ~10–25%, and it forms hard pan in soil plough (7–10 cm) layer due to increased soil bulk density. Water stagnation under continuously flooded PTR is the major source of methane emissions with serious environmental implications. Methane emissions from flooded rice can increase global warming potential by 18.1–27.6% compared to intermittently flooded rice with multiple aerations. The conventional tillage can favor the germination of grassy weeds in wheat, while the broad-leaved weeds increase under zero tillage. Zero tillage with mulch load conserved ~4.0% higher moisture due to ~2.3% lesser soil temperature and evaporated ~27.6% lesser than the conventional tillage. Delayed rice transplanting with short-duration variety has potential of saving of up to ~140 mm of irrigation water in the semiarid areas of NW IGPs. Although the DSR had lower yield potential than the PTR, it saved ~50% irrigation water. The laser land leveling technology saved ~30% irrigation water and ~25% electricity and had a yield advantage of ~4%, compared with PTR on un-leveled fields. The mechanical transplanted rice had higher grain yield and more water saving than the manual transplanting or DSR. The review demonstrates that a single technology may not be applicable everywhere and integrated approaches with the multiple criteria—productivity, economics, energy and environmental sustainability—would be required to address the unsustainability issues of the R–W system of the NW IGPs. There is a need to elucidate and disseminate various site- and context-specific RCTs appropriate for the region to address the unsustainability issues and challenges of the system. Sustainable R–W production technologies with reduced water, energy and C footprints are required for increased water and energy productivity and C sequestration for the NW IGPs of South Asia.