Health risks associated with the chronic, low-dose uptake of arsenic (As) have been of great concern in Southeast Asia, where rice is a staple crop. Arsenic is highly mobilized when paddy soil is flooded, causing increased uptake of As by rice. In this study, we investigated factors controlling soil-to-solution partitioning of As under anaerobic conditions. Changes in As and iron (Fe) speciation due to flooded incubation of two paddy soils (soils A and B) were investigated by HPLC/ICP-MS and XAFS. With the decline of Eh, As(V) in the soil solid phase was transformed to As(III). The fraction of As(III) in the soil solid phase was increased up to 80% of the total As in the soils. The increased pH due to flooded incubation resulted in an increased release of both As(III) and As(V) from soil to solution. The soil-to-solution partitioning of As(III) was greater than that of As(V). The Fe K-edge EXAFS spectra of soils A and B were similar before incubation, and ferrihydrite was the major component in the soils. After flooded incubation, siderite was detected only in soil A but not in soil B. In addition, the dissolved concentration of As was lower in soil A than in soil B. These results suggested that secondary formation of siderite prevented the dissolution of Fe as well as of As(III).