Nanobubbles (NBs) with a diameter of <1 μm have unique properties, including a long lifetime in water. Our previous study showed that irrigation with water containing bulk oxygen NBs (oxygen NB water) reduced seasonal methane (CH4) emissions from flooded rice cultivation by 21%. We therefore hypothesize that the CH4 emission reduction attributed to soil oxidation. To test this hypothesis, we carried out three sequential soil-column experiments under flooded and rice-unplanted conditions. They shared the same experimental settings, except for the lengths of soil storage before experiment (2–3 years) and of aerobic soil preincubation (7–13 days). The columns were manually irrigated with aerated tap water (control) or oxygen NB water. A tubing pump was operated to constantly drain leaching water from the column bottom. During the 57-day experimental periods, we regularly measured dissolved greenhouse gases in the drainage and leached heavy metals. The greater amount of leached manganese than of leached iron indicates that the reductive soil conditions were relatively weak in the three experiments. Oxygen NB water reduced the total dissolved CH4 emissions by 20–28% compared to control water. However, a significant difference (p < 0.05) was found only when the CH4 emission was greatest in the experiment with the shortest length of soil storage due to a high availability of soil labile carbon. Soil oxygen profiling using a microelectrode revealed that oxygen depletion at shallow depths (4–15 mm from the soil surface) was ameliorated by oxygen NB water on day 35 of experiment when the CH4 emission was smaller due to a limited soil labile carbon. The results confirm that irrigation with oxygen NB water reduces CH4 production in a flooded paddy soil through the oxidation of shallow soil.