Zinc (Zn) deficiency is a widely occurring constraint for rice production and for human nutrition. Scarcity of water is leading to a shift from flooded to aerobic rice production, which can have an impact on Zn deficiency in rice. Zinc bioavailability is a function of both soil and plant factors that can be altered by water management, particularly in relation to conditions in the rhizosphere. Biogeochemical modeling based on bulk soil conditions failed to predict the effect of water management on Zn bioavailability, but revealed that dissolved organic anions, pH, and redox conditions were major determinants. Rhizosphere sampling is needed to understand the difference in Zn mobilization and uptake between flooded and aerobic cultivation systems. Zinc bioavailability is not only affected by changes in the chemical properties of the soils, but also by biological processes such as mycorrhizal inoculation and root release of organic compounds into rhizosphere. Phytosiderophores and organic acids are two classes of Zn chelators secreted from roots that have been linked to the release of Zn from soil-bound forms and its subsequent uptake by plants. A shift to aerobic condition provides a favorable environment for activity of mycorrhizal fungi and enhanced mycorrhizal inoculation under aerobic conditions has been shown to increase plant Zn uptake. Aerobic rice genotypes with varying tolerance to Zn deficiency display a trade-off between mycorrhizal Zn responsiveness and root exudation of Zn chelator in the rhizosphere, which is probably due to a competition for carbon. Potential agronomic management practices in aerobic rice production systems are discussed, with an emphasis on their roles in improving bioavailability of Zn. Addition of Zn fertilizers by soil or foliar application have been shown to increase Zn concentration in cereal grains but the extent of the increase differs among crop species. The shift from flooded to aerobic condition can cause significant N transformations, which may consequently affect Zn mobilization and uptake. An appropriate N management strategy, including an effective combination of source, rate, application method, and timing, should consider the effects on soil pH. Application of P fertilizer should be done with careful consideration to the effect on Zn uptake. A reasonable cropping system (intercropping and crop rotation) could prevent Zn deficiency and offer an effective and sustainable pathway to Zn biofortification. Keeping these points in mind, this review describes our current knowledge of Zn bioavailability as affected by changes in soil–plant interactions caused by the transition from flooded to aerobic rice cultivation.