Aquaponics is a promising technology combining aquaculture with hydroponics. In this study, algal-bacterial consortia were introduced into aquaponics, i.e., algal-bacterial based aquaponics (AA), to improve the nitrogen utilization efficiency (NUE) of aquaponics. The results showed that the NUE of AA was 13.79% higher than that of media-based aquaponics (MA). In addition, higher NO3- removal by microalgae assimilation led to better water quality in AA, which made up for the deficiencies of poor aquaponic management of nitrate. As a result of lower NO3- concentrations and dramatically higher dissolved oxygen (DO) concentrations caused by microalgae photosynthesis in the photobioreactor, the N2O emission of AA was 89.89% lower than that of MA, although nosZ gene abundance in MA's hydroponic bed was approximately 30 times over that in AA. Considering the factors mentioned above, AA would improve the sustainability of aquaponics and have a good application foreground.