Aquaponics combines the hydroponic production of plants and the aquaculture production of fish into a sustainable agriculture system that uses natural biological cycles to supply nitrogen and minimizes the use of nonrenewable resources, thus providing economic benefits that can increase over time. Several production systems and media exist for producing hydroponic crops (bench bed, nutrient film technique, floating raft, rockwool, perlite, and pine bark). Critical management requirements (water quality maintenance and biofilter nitrification) for aquaculture need to be integrated with the hydroponics to successfully manage intensive aquaponic systems. These systems will be discussed with emphasis on improving sustainability through management and integration of the living components [plants and nitrifying bacteria (Nitrosomonas spp. and Nitrobacter spp.)] and the biofilter system. Sustainable opportunities include biological nitrogen production rates of 80 to 90 g·m−3 per day nitrate nitrogen from trickling biofilters and plant uptake of aquaculture wastewater. This uptake results in improved water and nutrient use efficiency and conservation. Challenges to sustainability center around balancing the aquaponic system environment for the optimum growth of three organisms, maximizing production outputs and minimizing effluent discharges to the environment.