In aquaponics, your invisible little helpers are the nitrifying bacteria in your oxygenated water. What you do not want in your water or anywhere in your aquaponic system are soil pathogens that will interfere with the activities of your nitrifying bacteria.
So contact with unsterilized soil is not advisable in aquaponics. You just do not know what is in that soil that might make war on your nitrifying bacteria, eat the roots of your plants (slugs and snails, nematode worms, etc) and grow mushrooms on your crops.
If you are using ponds for your fish, the water in the ponds is in contact with soil. That is dirt to the uninitiated. In a highly intensive high fish stocking rate aquaponic system, you just do not want anything in there that is unaccounted for. That is why you have the solids removal systems with its clarifier and orchard netting tanks, to remove the fish solid poo before it develops hitch hikers. Not just because it will also clog up your pipes something rotten.
You just want liquid fertilizer going round your hydroponic tanks with no swimmers. I stress tanks, they are easy to clean and you can see what is going on in there, just lift a floating raft. You need to be able to control the pH of the water in the tanks. You will need to use a simple pH meter like the one pictured here very frequently to get some idea of where the biology of your tanks is going. This is vital if your fish and plants are going to grow and live together. So you do not want anything seeping in through a soil pond wall that will affect the acidity or alkalinity of the water, such as floodwater or sewage. You need a neutral inert waterproof wall to your TANK. You need to keep the pH of your water at 7.0 or thereabouts constantly for aquaponics to work for both fish and plants.
You also do not want any parasites in the water that will come from soil and attach themselves to the fish, causing fish diseases.
Soil is out. You cannot use soil ponds in aquaponics.
You can use holes in the ground, properly reinforced and then lined with plastic special pond liner. That is what they do at Growing Power and Sweetwater Organics in Milwaukee very successfully. But those rectangular fish raceways are lined with heavy duty pond liner which is easy to clean and stands up to a lot of punishment.
Earth ponds are just too close to all the natural variables like the wrong sort of parasitic worm that will hatch out in your fish and spread. You cannot use antibiotics or vermicides, they will kill your little nitrifying bacterial helpers, that turn the fish waste into plant food for your crops. Conversely, ‘organic’ pesticides based on pyrethrum flowers are instantly lethal to fish. You can use parasitic wasps and ladybugs to control greenfly, lacewings which eat thrips as well, and so on. But my greenfly this year outlived my ladybugs, and I have been going around washing them off the leaves of my water spinach and basil by hand, a very time consuming process.
Without healthy plant growth, you will start to experience nitrite and ammonia spikes in your aquaponic system’s water, which can kill your fish. Tanks full of dead fish stink.
So you need to keep the soil and its pest load well away from your aquaponic system. No soil and clay ponds please. Clean tanks rock.