Flooding induces significant chemical changes in soil due to the weakness of gas transfer between soil and atmosphere. Thus, pCO2 increases in solution while pO2 and redox potential decrease. In an alkaline soil, this can lead to great variations of alkalinity. Increase in pCO2 leads to a decrease in pH, a dissolution of alkaline minerals, like calcite, and an increase in alkalinity. Decrease in potential redox is related to reduction of Fe(III) that produce alkalinity in soil solution. This reduction of Fe is supposed to take place both: in the structure of ferriferous clay minerals that induces an increase in the Cationic Exchange Capacity; and in a crystalline structure, natural Fe(II)-Fe(III) green rusts that induces a decrease in Anionic Exchange Capacity. The influence of these processes has been evaluated through laboratory and field experiments under flooded rice cropping system in the Office du Niger perimeters in Mali. The results allow to model the alkalinity balance in such alkaline soils: alkalinity is produced in soil solution, diffuses to the flood water and finally is flushed toward the drainage system. These mechanisms are able to ensure the sustainability of irrigated schemes faced with alkalinisation hazard.