Micro-nano bubbles (MNBs) have emerged as a promising and sustainable gas–liquid phase technology, which is attracting increasing attention for their applications in aquatic ecosystem restoration. These include high gas–liquid mass transfer efficiency, prolonged residence time in water, exceptional stability, and distinctive interfacial zeta potential. These characteristics significantly influence their physical and chemical behavior in aqueous environments. Bulk MNBs can rapidly increase oxygen concentration to enhance oxygenation, produce strong reactive oxygen species for organic pollutant degradation without secondary pollution, remove algae and support plant growth and ecosystem recovery. In contrast, interfacial NBs can improve anoxic sediment conditions through physical separation, adsorption, and a sustained oxygen supply. They can also regulate microbial communities and reduce the flux of nutrients (i.e., nitrogen and phosphorus), as well as mitigate heavy metal contamination and greenhouse gas emissions. These insights aim to support both theoretical research and the practical utilization of MNBs in environmental engineering and related disciplines.