A set of long-term experiments with irrigated rice (Oryza sativa L.) in the Philippines provides an opportunity to assess the sustainable management of intensively cultivated lowland rice ecosystems. We assessed sustainable management from the capability of the ecosystem to maintain a supply of plant-available nutrients, the changes in soil organic matter and soil properties, the long-term trends and stability in crop yields, and the efficiency of input use. Plant-available nutrients in rice ecosystems originate from soil organic matter and soil minerals, crop residues and manures, biological N2 fixation, irrigation water and sediments, and fertilizers. Nutrients arising from all sources other than fertilizers are referred to as the indigenous nutrient supply.

Long-term experiments in the Philippines reveal that soil submergence during intensive rice production acts to maintain soil organic matter, sustain indigenous N supply, and promote biological N2 fixation. After an initial equilibration period, yields did not decline in the past 30 years in systems with continuous cultivation of two or three rice crops per year and adequate fertilizer inputs — even when all aboveground plant biomass was removed. Soil organic matter levels were sustained in these intensive rice monoculture systems in the past 20 years. Indigenous N supply as determined by N mineralization and yield of rice not receiving fertilizer N was stable during 30 years of continuous cultivation of two and three rice crops per year even when aboveground plant biomass was removed. Water management and tillage practices in the interval between rice crops markedly influenced indigenous N supply, the yield of rice without fertilizer N, and hence the plant need for fertilizer N.

Fluctuation in climate, especially solar radiation, was a major factor contributing to year-to-year variation in rice yield. The timely input of nutrients, especially N, was required to sustain high yields. Rice yield a long-term experiment was increased in superimposed plots with dynamic application of fertilizer N based on leaf N status, indicating scope for additional gains in rice yield through improved N management that accommodated the real-time needs of the crop for added N.

Diversification from continuous rice cropping on submerged soil to rotation of rice with an upland crop grown on aerated soil can markedly alter soil C and N dynamics. The conversion from rice–rice monoculture to rice–maize rotation led to about a 15% reduction in soil C and a decline in N mineralization during the rice crop. More soil nitrate accumulated after the maize than rice crop, and this nitrate was lost presumably by denitrification upon flooding the soil for rice cultivation. Indigenous N supply as determined from yield of rice not receiving fertilizer N was consistently lower following maize than rice in the past eight years of an eleven-year experiment. Yield of fertilized rice was equally high following rice and maize — provided fertilizer inputs were sufficient. More fertilizer N was required for rice following maize than rice. The trend in Asian lowland rice ecosystems to greater soil aeration as a result of diminishing supply of irrigation water and diversification to other crops could lead to reduced soil organic matter and soil nutrient supplying capacity in one of the most important and productive agricultural production systems in the world.