In the rainfed lowlands of South-East Asia, rice yields are low and often respond weakly to fertilizers. Studies of soils in Cambodia and North-East Thailand suggest that a complex combination of factors restrict rice yield and nutrient uptake in response to loss of soil-water saturation. Two significant and closely linked constraints are viable rainfall and lack of soil nutrients. Intermittent flooding and drying of soils depresses availability of some nutrients, even when water supply is adequate. Moreover, extreme fluctuations in soil-water levels may impair root activity, further restricting nutrient uptake. The resulting inefficient uptake apparently leads to weak responses to fertilizer nitrogen and phosphorus. Developing management strategies for optimizing the mineral nutrition of rice in drought-prone rainfed lowlands, particularly in the presence of aluminium toxicity and potassium deficiency, thus depends on understanding the function of rice roots in nutrient uptake and their response to temporal and spatial variation in water content and soil properties. This need is particularly relevant for the adoption of direct sowing of rice, which results in a root system developing initially in aerobic conditions, then being exposed to flooded conditions and, during the growing season, returning to aerobic and, in extreme cases, to drought conditions. With the potential increase of fertilizer use in the future, and thus potential pollution of groundwater and eutrophication of water bodies, new management strategies also need to assess risks of such contamination and seek ways of preventing it.