In rice production, monoculture is the norm in irrigated paddies. Because rice varieties are selected for productivity and are further interbred to maximize this trait, there is growing concern that the genetic pool has shrunk. In the process of creating uniform high-yield varieties, plant characteristics which existed in traditional rice strains (such as pest resistance) may have disappeared

One of the principal techniques in modern rice culture is soil puddling. This method enables the planting of as many as three crops per year instead of a single annual harvest. It has, however, the effect of excluding the traditional practice of crop rotation whereby soil was naturally refurbished with nitrogen and other organic nutrients from other plants. Synthetic fertilizers, especially nitrogen, phosphorus and potassium, have to be applied in increasingly bigger doses to offset the rapidly deteriorating condition of the soil. Repeated agrochemical applications in turn lead to the disappearance of another important natural source of nutrients, the nitrogen-fixing algae in the soil

Over 1,000 species of predators and parasites have been identified in the traditional rice culture, including nitrogen-fixing algae, humus building agents, and natural enemies of rice-attacking pests. Repeated use of fertilizers, insecticides, molluscicides, herbicides and rodenticides has indiscriminately decimated the number and type of rice paddy inhabitants. The introduction of heavy machinery compacts the soil in paddies as well as neighbouring fields, increasing soil runoff, hence erosion and agrochemical pollution, and hampering soil aeration, root growth and penetration. The disappearance of nutrient-manufacturing algae and vegetation deprive rice plants of naturally fertile ground, while the loss or contamination of water reptiles, fish, frogs and snails deprives people of an important food source. Organochloride insecticides were found in about half of farmers' blood samples

Irrigated rice production competes with other activities for the use of water. In the Philippines, in line with the national policy of self-sufficiency in rice, canals were constructed to irrigate rice paddies, thereby diverting water from other uses including non-rice crops. In Thailand, however, under the pressure of water shortages, the Government decided to allow available water in the rice-growing basins to be used for non-agricultural purposes. Because of this, for example, in the 1993 dry season, the second rice crop was expected to be small. From an environmental point of view, this approach is positive as double-cropping of irrigated rice is ecologically less stable that rice cultivation in a rainy season only

Rotating rainy season rice with other crops in the dry season would impede the survival of rice pests, limit methane emission and improve physical and chemical properties of the soil. Rotation with leguminous crops could meet the nitrogen requirement of the rice crop; as would incorporation of rice straw (often otherwise polluting agricultural waste) as mulch and humus-building material