Vivianite is a hydrated ferrous phosphate mineral that can form in reducing environments, and it was recently identified on aged paddy rice (Oryza sativa, L., cultivar Hitomebore) roots. However, the formation and dissolution of vivianite appear highly susceptible to the soil redox potential. We examined the effect of water management on the vivianite content of rice roots in three experimental micro (1 m2) paddy fields. The vivianite content of the roots was estimated using a method based on the alteration of vivianite after heating at 105°C for 48 h. This alteration steeply lowers the dissolution of phosphate from the roots in a mixed acid solution of 0.1 mol L−1 of hydrochloric acid (HCl) and 1 mol L−1 of acetic acid (CH3COOH). Efficiency of the method was confirmed regarding heating temperature and duration of heating. Using this method, we found that water management significantly influenced the vivianite content of the rice roots. The vivianite content of the rice roots was highest, i.e., 2.3 g phosphorus (P) kg−1 expressed by its estimated P content, when the paddy field was continuously flooded from May to until early September. After flooding stopped, the soil was gradually oxidized, leading to a decrease in vivianite content. In the micro plot exposed to midseason drainage, the vivianite content increased to the level of the continuously flooded plot after reflooding, and finally decreased after flooding was stopped in late August. The plots exposed to midseason drainage followed by intermittent irrigation presented the lowest vivianite contents among the three experimental paddy fields. These results confirm that increases and decreases in the vivianite contents of paddy-rice roots strongly depend on water management.