Aquaponics has ancient roots, although there is some debate on its first occurrence.
Aztec cultivated agricultural islands known as chinampas and are considered by some as the first form of aquaponics for agricultural use where plants were raised on stationary (and sometime movable) islands in lake shallows and waste materials dredged from the Chinampa canals and surrounding cities are used to manually irrigate the plants.

South China and Thailand who cultivated and farmed rice in paddy fields in combination with fish are cited as examples of early aquaponics. These polycultural farming systems existed in many Far Eastern countries and raised fish such as the oriental loach swamp eel , Common and crucian carp as well as pond snails in the paddies.
Diagram of the University of the Virgin Islands commercial aquaponics system designed to yield 5 metric tons of Tilapia per year.

The development of modern aquaponics is often attributed to the various works of the New Alchemy Institute and the works of Dr. Mark McMurtry et al. at the North Carolina State University. Inspired by the successes of the New Alchemy Institute, and the reciprocating aquaponics techniques developed by Dr. Mark McMurtry et al., other institutes soon followed suit. Starting in 1997, Dr. James Rakocy and his colleagues at the University of the Virgin Islands researched and developed the use of Deep Water Culture hydroponic grow beds in a large scale aquaponics system.

The first aquaponics research in Canada was a small system added onto existing aquaculture research at a research station in Lethbridge, Alberta. Canada saw a rise in aquaponics setups throughout the '90s, predominantly as commercial installations raising high value crops such as trout and lettuce. A setup based on the deep water system developed at the University of Virgin Islands was built in a greenhouse at Brooks, Alberta where Dr. Nick Savidov and colleagues researched aquaponics from a background of plant science. The team made findings on rapid root growth in aquaponics systems, on closing the solid waste loop, and that because of certain advantages in the system over traditional aquaculture, the system can run well at a low pH level, which is favoured by plants but not fish.

The Edmonton Aquaponics Society in Northern Alberta is adapting Dr. Savidov's commercially sized system to a smaller scale prototype that can be operated by families, small groups, or restaurants. They intend to further develop the closed solid waste loop.