Excessive application of chemical fertilizers can lead to serious environmental problems. In this study, we explored the use of nanobubble water for irrigation of crop rice as a means of reducing fertilizer use. The effect of nanobubbles on plant growth and nutrient uptake was evaluated in the laboratory, while crop yield and the efficiency of fertilizer use were evaluated in a field study. The laboratory experiments indicated that nanobubbles significantly improve plant height and root length in rice seedlings. Nanobubble treatment stimulated synthesis of the growth hormone gibberellin and upregulated the plant nutrient absorption genes OsBT, PiT-1 and SKOR, resulting in increased nutrient uptake and utilization by the roots. The field experiments verified the laboratory observations, showing that nanobubble treatment significantly increases rice yield by almost 8% when using similar levels of fertilizer as controls. Moreover, the same yield as controls was achieved with approximately 25% less fertilizer. As well as their impact on growth hormones and nutrient absorption genes, nanobubbles, due to hydrophobic and surface charge properties, enhance the release and absorption of soil nutrients, thereby reducing fertilizer demand. Overall, this study highlights a new and sustainable water irrigation strategy for enhancing crop yield and reducing chemical fertilizer waste.