Green revolution technologies of the 1960s and 1970s have led to the emergence of rice (Oryza sativa)–wheat (Triticum aestivum) (R–W) as a major cropping system in the Indo-Gangetic Plains (IGP). Expansion of irrigation through a network of canals and privately owned tube wells was one of the key factors in the success of the new technologies. Since canal water supplies are not demand-driven, farmers increasingly relied on the use of ground water by installing shallow tube wells. The strategy of ground water development and its use in conjunction with canal supplies paid rich dividends in control of waterlogging and secondary alkalization and in increasing the pace of alkali soils reclamation programmes in areas underlaid with fresh quality aquifers. Rice–wheat systems were the preferred choice of farmers. Adoption of the R–W system, however, changed the salt and water balance in north-western parts of the IGP. In the north-east of Punjab and Haryana states it led to receding water tables and waterlogging, and in south-west parts to associated problems of secondary salination. In eastern parts of the IGP in West Bengal, development of ground water aquifers to meet irrigation water requirements for the intensification and diversification of agriculture has led to serious problems of ground water contamination due to dissolution of arsenic-bearing minerals under altered soil moisture regimes, conducive to oxidation of pyritic sediments. These experiences suggest that there is an urgent need for a change in the way food is produced in the IGP for sustainability of the natural resource base. This will depend on the ability to predict long-term consequences of intensification and diversification of agriculture on the farm and regional scale. Whereas issues of favourable regional salt and water balances need attention in the north-west of the IGP, rain-water management and alleviating drainage congestion can facilitate the adoption of agricultural technologies and improve productivity of the R–W systems.