Rice (Oryza sativa L.) and wheat (Triticum aestivum L.) are now grown in sequence on the same land in the same year around the world to meet the food demand of a rapidly growing human population. The challenges in rice and wheat research are to understand crop responses to the required combination of practices. As such management systems can be devised for high and sustainable combined yield. The repeated transitions from anaerobic to aerobic and vice versa affect soil structure, nutrient relations, the growth of the component crops, and their associated pests and diseases. Rice and wheat research should concentrate on soil, water and nutrient management strategies including reduced tillage and use of raised beds, that avoid the deleterious effects of puddling on soil structure and fertility, improve water and nutrient-use efficiencies to increase crop productivity of both rice and wheat.