The pressure to find effective strategies for the sustainable transformation of agricultural systems is higher than ever. Combining different production systems and using their respective wastes to produce more with fewer resources is the concept of aquaponics. Aquaponics is a biological process that involves recirculating aquaculture (RAC) and the production of vegetables, flowers, and herbs. Several scientific reports and observations by growers show that aquaponics can be considered as a very suitable model for food production in a sustainable way. Aquaponics can be used as an efficient method of food production by following several ecological principles such as waste generation by one biological system that may serve as a source of nutrients for another biological system by the activity of appropriate microbes and their coordinated activities. Integration of fish and growth of plants on fish waste is like a multitrophic ecosystem that leads to diversity and increases yield of multiple products. Wastewater generated in aquaculture is re-used through biological filtration and recirculation process. This results in localized food production throughout the year and provides healthy foods to the local community and boosts their economy. This review aims to discuss the recent scientific technologies, trends in implementation, and ideas of aquaponic food production, role of microbes and algae in waste recycling and system operation and the beneficial effect on the environment.