Hydroponics and aquaponics. hydroponics and aquaponics can both result in better growth of plants. water rich in nutrient with a high level of oxygen is used. though both use soil-free way to cultivate the crops, there’s still differences between the two systems. aquaponics uses hydroponic environment with the fishes whereas hydroponics does not need the presence of animals.. Starting up your aquaponics system involves making sure that the bacteria grows and thrives in your system, and you will need to give it some time before the population of bacteria can support fish and plant growth. as soon as you put fish in your tanks, they will start producing ammonia (in their wastes)..