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A remarkable feature of nanobubbles (<10^–6 m in diameter) is their long lifetime in water. Supplying oxygen-nanobubbles (NBs) to continuously flooded paddy soil may retard the development of reductive conditions, thereby reducing the emission of methane (CH₄), a potent greenhouse gas, and dissolution of arsenic, an environmental load. We tested this hypothesis by performing a pot experiment and measuring redox-related variables. The NBs were introduced into control water (with properties similar to those of river water) using a commercially available generator. Rice (Oryza sativa L.) growth did not differ between plants irrigated with NB water and those irrigated with control water, but NB water significantly (p < 0.05) reduced cumulative CH₄ emission during the rice-growing season by 21%. The amounts of iron, manganese, and arsenic that leached into the drainage water before full rice heading were also reduced by the NB water. Regardless of the water type, weekly-measured CH₄ flux was linearly correlated with the leached iron concentration during the rice-growing season (r = 0.74, p < 0.001). At the end of the experiment, the NB water significantly lowered the soil pH in the 0–5 cm layer, probably because of the raised redox potential. The population of methanogenic Archaea (mcrA copy number) in the 0–5 cm layer was significantly increased by the NB water, but we found no correlation between the mcrA copy number and the cumulative CH₄ emission (r = –0.08, p = 0.85). In pots without rice plants, soil reduction was not enhanced, regardless of the water type. The results indicate that NB water reduced CH₄ emission and arsenic dissolution through an oxidative shift of the redox conditions in the flooded soil. We propose the use of NB water as a tool for controlling redox conditions in flooded paddy soils.