Micronutrients play an active role in the plant metabolic processes starting from cell wall development to respiration, photosynthesis, chlorophyll formation, enzyme activity, nitrogen fixation and reduction etc. Micro nutrient requirements of the crops are relatively small and ranges between their deficiencies and toxicities in plants and soils are rather narrow. Transformation and behavior of micro nutrients in submerged soils are entirely different compared to normal soils. The electrochemical and biochemical changes caused by submergence directly and indirectly influence the solubility and availability of micro nutrients in the soil. Submergence increases the availability of Fe, Mn, and molybdenum but decrease the availability of B, Zn and Cu. The most important effect of submerging a soil in water is a cut in the oxygen supply and quickly it goes devoid of oxygen. The exhaustion of oxygen causes reduction of soil and sets in motion a series of physical, chemical and biological process that profoundly influence the quality of a soil as a medium for plant growth, especially for crops like rice.