Aquaponics is a climate-smart food production system that relies on nutrient recovery from aquaculture effluent. The availability of dissolved oxygen (DO) limits the performance of aquaponic systems. To address this issue, air micronanobubbles (MNBs) were tested as an alternative aeration method. Due to their small size (<50 μm) and long-term stability, MNBs can enhance the gas−liquid mass transfer of oxygen and maintain DO concentrations above saturation, enhancing aerobic biochemical processes. Through 16S rRNA gene metabarcoding and water quality analyses, we investigated the influence of continuous MNB aeration on DO concentrations and carbon−nitrogen cycling. Our results indicated that continuous MNB aeration (K L a 20 = 7.76 ± 0.38 h −1 ) in the grow bed of an aquaponic system increased DO concentrations to 9.31 ± 1.57 mg L −1 without affecting other system components. In comparison, aeration with a conventional diffuser (K L a 20 = 1.73 ± 0.54 h −1 ) maintained lower DO concentrations of 6.32 ± 0.32 mg L −1 on average. Further benefits of MNBs include higher reductions in total solids (16 ± 2%) and volatile solids (32 ± 2%) and an increase in nitrate concentrations over time. Notably, MNB aeration enhanced the total butterhead lettuce yield and root biomass per plant by 35 ± 8% and 20 ± 5%, respectively. While MNB aeration reshaped the microbial community and potentially disturbed certain microbial symbiotic relationships (e.g., Denitratisoma, Thermomonas, and Nitrospira), the overall metabolic pathways remained largely intact. Overall, our study provides insights into the application of MNB aeration to enhance plant biomass production in floating raft aquaponic systems and increase nitrification and remineralization.