Rather than direct nutrient removal from wastewaters, an alternative approach aimed at nutrient recovery from aquacultural wastewaters could enable sustainable management for aquaculture production. This study demonstrated the feasibility of cultivating marine macroalgae (Chaetomorpha maxima) with a moving bed bioreactor (MBBR-MA), to remove nitrogen and phosphorus in aquaculture wastewater as well as to produce macroalgae biomass. MBBR-MA significantly increased the simultaneous removal of nitrate and phosphate in comparison with only MBBR, resulting in an average total nitrogen (TN) and total phosphorus (TP) removal efficiency of 42.8±5.5% and 83.7±7.7%, respectively, in MBBR-MA while MBBR had no capacity for TN and TP removal. No chemical oxygen demand (COD) removal was detected in both reactors. Phosphorus could be a limiting factor for nitrogen uptake when N : P ratio increased. The recovered nitrogen and phosphorus resulted in a specific growth rate of 3.86%–10.35%/day for C. maxima with an uptake N : P ratio of 6. The presence of macroalgae changed the microbial community in both the biofilter and water by decreasing the relative abundance of Proteobacteria and Nitrospirae and increasing the abundance of Bacteroidetes. These findings indicate that the integration of the macroalgae C. maxima with MBBR could represent an effective wastewater treatment option, especially for marine recirculating aquaculture systems.