The performance of microalgae aquaculture wastewater treatment system predominated mainly by Scenedesmus and Chlorella was assessed. Treatment induced a progressive reduction in both COD and BOD to values below the discharge limits. Different patterns were obtained for removal of phosphorus, nitrogen, and ammonia; however, the algal culture efficiencies reached 100% in their removal by the end of the treatment period. The applied aquatic systems demonstrated percentage reduction of heavy metals in the range between 52.3 and 100% in the batch system and 64.2 and 100% in the continuous system. Wastewater supported algal growth by inducing the incorporation of a significantly higher content of the individual amino acids Asp, Thr, Ser, Glu, Gly, and Tyr, and a markedly higher level of Pro. However, His, Lys, and Arg were markedly reduced compared to their levels in synthetic-medium-grown algae.