The continuous flooding of rice fields without an adequate drying period has negative effects on other chemical and biological processes within the soil

Water management is the key to creating sustainable rice-based production systems, particularly because rice is the only major cereal that can withstand water submergence.

For thousands of years, natural selection pressures such as drought, submergence, flooding, nutrient stresses, biotic stresses and human intervention have contributed to the great diversity in rice varieties and rice ecosystems. Based on their diversity, rice agronomists and ecologists have proposed several classification systems, of which the most widely used distinguishes five water related categories: rain-fed lowland, deep water, tidal wetlands, upland and irrigated rice. During the 1990s, only about 11% of the world's rice harvested areas were upland; the remaining harvest came from water-flooded systems.

The topography of the local landscape within which rice is cultivated has led to the development of specific water management and cultivation practices that produce specific beneficial outcomes. The terrace system in mountainous areas is a typical product of the ponding technique which has allowed cultivation even on steep slopes.  This technique is instrumental in preventing soil erosion and landslides. Another advantage of this technique is its capacity for flood control: the field bunds have a high water storage capacity which reduces peak flows under heavy rains. The layer of water due to ponding in rice cultivation minimizes weed growth and thus also the need for herbicides and manual weed control. The permanent presence of water on the field also generates percolation of water and groundwater recharge, which is often beneficial for other types of water use.

The complexity of the relationship between rice and water is well exemplified in rice-based systems with soil submersion. Submerged conditions enable organic matter to accumulate in soils, which contribute to carbon sequestration. In submerged systems, soil organic matter serves as a nutrient reservoir and provides rich sources of mineral elements for plants. However, the continuous flooding of rice fields without an adequate drying period has negative effects on other chemical and biological processes within the soil, such as a retarded rate of humus decomposition, a decreased rate of soil nitrogen mineralization, salinity build up and water logging. In addition, wetland soils are known for methane emission, a greenhouse gas. Finally, the continuous presence of water encourages the occurrence of disease, such as malaria, while this very same water presence supports natural predators for mosquitoes (the malaria carriers) and allows farmers to supplement their livelihoods from the rice-based systems' agro-biodiversity.

The seemingly contradictory advantages and disadvantages that submerged rice systems have on people and the environment can be better resolved through good agriculture practices. Rice-based systems have been designed to use freshwater resources for multiple purposes and to support the biodiversity that originally relied upon the natural aqua-ecosystem while also enabling intensive rice cultivation systems that include fisheries, livestock, and plant species.