Miniature air bubbles with a diameter of less than 200 nm were generated by a nanobubble aerator, and nanobubble water (NBW) was eventually obtained using the gas-liquid mixing system with hydrodynamic function. As the air bubbles have long lifetime and high gas solubility in the liquids, NBW is stable in nature and inside contains sufficient dissolved oxygen. At present, there is no report on the use of NBW to replace ordinary water to cultivate microalgae. In this research, effect of NBW on the growth and metabolism of different microalgae, including Haematococcus lacustris and Botryococcus braunii was investigated. The result demonstrated that the growth of H. lacustris and B. braunii was increased by NBW and the highest promotion ratio was up to 44% and 26%, respectively. For H. lacustris, the astaxanthin content in the NBW treatment group was also improved compared to the control group. As the main product of B. braunii, lipid content in the dry matter was decreased after the treatment of NBW, but total lipid production was significantly higher than that of the control group. In general, NBW could serve as the potentially effective tool to promote the growth of microalgae in the future.