Nickel (Ni) is an essential micronutrient for plants although it is considered toxic when present in excess in the soil. This study investigated the transfer of Ni from the soil to rice in terraced paddy fields affected by serpentinite, which contains an anomalously higher Ni content compared with other geological materials. Soils, soil solutions, and rice plants were collected at several different growing stages from three adjacent terraced paddy fields subject to the same water and fertilizer management. Temporal changes in their elemental compositions revealed that a higher concentration of Ni was dissolved in the soil solution during flooded conditions, probably due to the co-solubilization with Mn oxides under low redox potential conditions. However, rice accumulated Ni at a higher rate during the drainage period than in the flooding period. Although the Ni concentration in the soil solution was lowest in the drainage period, the relative concentration to Fe (i.e., Ni/Fe ratio) was much higher than that in flooded conditions. These relationships suggest that a potential measure to counter the transfer of Ni from the soil to rice in serpentine-affected paddy fields is to increase Fe phytoavailability during the drainage period.