Flooded rice soils produce elevated concentrations of soluble manganous manganese (Mn2+) that could be potentially toxic to subsequent crops. To provide insight into how soil pore Mn2+ changes its concentration in a rice and post rice drying soil, we used an artificial microcosm system to follow Mn2+ concentrations in two different soil types (red sodosol and grey vertosol) and under two irrigation regimes (flooded and saturated). Soil pore water was collected from four different depths of soil (2.5 cm, 7.5 cm, 15 cm and 25 cm) and Mn2+ concentrations were analysed during and after the rice phase over a one year cycle. Mn2+ increased with the advancement of anaerobic conditions at all soil depths, but the concentration was higher in flooded soil compared to saturated soil. Initially, the highest concentration of Mn2+ was found at a depth of 7.5 cm, while at the later stage of rice growth, more Mn2+ was found in the deepest sampling depth (25 cm). Plants grown in saturated soils showed a delay in flowering of approximately 3 weeks compared to flooded cultures. Moreover, plants grown in flooded soil produced more tillers and leaf area than those grown in saturated soil. Peak concentrations of soil Mn2+ were associated with the reproductive stage of rice growth. Mn2+ concentrations decreased after drainage of water. In post rice soils, Mn2+ remained elevated for some time (lag phase), and then rapidly declined. Regression analysis revealed that the process of oxidation of Mn2+ to Mn4+ following water drainage decreased with soil depth.