The rapid development of aquaculture that is diverse in character brings more challenges for water resource management. Discharges from all aquaculture systems can be characterized by a high concentration of nutrients. This raises concerns not only about their toxicity, but also about eutrophication and ecological degradation. Various aerobic treatment technologies are presented in this chapter to tackle this problem. The treatment technologies are assessed based on five aspects-basic principles, design parameters, treatment efficiency, advantages, and disadvantages. While traditional biofiltration methods are still applied widely, more alternatives such as wetlands, membrane bioreactors, and aquaponics are being considered. Aerobic treatment is mostly effective at removing total ammonium nitrogen or, in other words, nitrification. It is not very efficient at removing nitrate and phosphorus, with the exception of some wetlands, innovative membrane biofilm reactors for denitrification, and aquaponics systems. Therefore, aerobic treatments need to be incorporated into a denitrification process.