Wastewater management and disposal in aquaculture is becoming increasingly important due to stringent water regulations regarding waste discharges into natural water systems. Recirculation aquaculture is one of the technologies designed to reduce waste discharge through the nitrification process. However, nitrification results in nitrate accumulation which is normally reduced by dilution through water exchange. Water exchange is only possible with sufficient water. Although nitrification is a conventional process, it has limitations because the autotrophic bacteria require long start-up and multiplication periods. The nitrifiers require high levels of oxygen with relatively higher aeration costs. Moreover, the bacteria are sensitive to rapid changes in pH, temperature, and flow rate. Denitrification can be a solution to the limitations of nitrification since denitrifiers are most abundant in the natural environment and have higher growth rates than nitrifiers. In addition, the process reduces energy costs since there is no need for aeration, water consumption is also reduced drastically since water exchange is minimized. Organic loading can be reduced when fish waste is utilized as a carbon source. An alternative process to manage aquaculture wastes is through anaerobic ammonium oxidation (anammox), where ammonia and nitrite are converted into nitrogen gas. Anammox can efficiently reduce ammonia and nitrites from culture water, but it has not received wide application in aquaculture. Aquaculture wastewater contains nutrients which are essential for plant growth. The plants maintain good water quality by absorbing the dissolved nutrients. Denitrification, anammox, and nutrient uptake by plants are feasible strategies to reduce wastes from aquaculture effluents.