While talking about Aquaponics this weekend at Boonville's annual Not So Simple Living Fair, I had two different people ask me about using their ponds to build an aquaponic system. While they are not the first to ask me about using ponds, they did get me to thinking that the subject is really more complicated than I can answer in an off the cuff couple sentences. For those of you who don't like to read, the short answer is that I have never used a natural pond, and I doubt I ever will for a whole variety of reasons. A pond engineered specifically for aquaponic use would be a different story.
I would like to start with the advantages a pond offers us when building an aquaponic system. First and most important is that ponds often already exist on a property, and we don't need to spend anything to build it. Ponds also can hold a whole lot of water, far more than most fish tanks I can think of, with perhaps the exception of a weld-wire and liner tank. The biggest reason for wanting a lot of water is to allow for a large growing area when using fill & drain style grow beds.
Unfortunately there are a lot of negatives attached to using ponds, particularly natural ponds. The first consideration is that normally we are mimicking nature when we build an aquaponic system, but we are also trying to separate it enough from nature that we can gain some control in order to optimize the operation. If you use a natural pond, you should expect nature to take advantage of the resources it provides - namely your expensive fish. Getting too cozy with nature also carries the risk of birds and animals introducing diseases to your system which will find it a perfect environment for explosive growth. Covering (see below) your pond might keep out a lot of the birds, and using a high voltage, low height "fence" would keep out most predators such as raccoons.
Often ponds are quite large, not just in terms of water volume, but also in terms of acreage. This presents a problem with managing sunlight because where ever the sunshine hits nutrient rich water, algae will rapidly grow. A little algae is good for your system, but a lot will kill everything including your fish and plants. The fish will die because the algae will absorb all available oxygen, suffocating your fish. The plants will die because they cannot compete with the algae for nutrients. This means that you will need to find a way to block 90-95% of the sun hitting the water. The cheapest way I know to do this would be with shade cloth and wires to hold it up.
If your pond is connected to the local watershed (it is fed by springs or feeds the local streams), you will have another set of problems to manage. The first one (in the USA) is dealing with Fish & Game which operates with the belief that they own and/or manage all waterways regardless of where they are in the US. You would of course want to talk to someone more knowledgeable with regulations in your area, but I would hazard to guess that there will be trouble eventually if you stock your pond with non-native fish, if you allow nutrient rich water (high levels of nitrates primarily) to wash down stream, or if you try to harvest your own fish without a license (fishing license that is). While you might not feel that the harvesting fish will be a big deal, but the other two concerns are a really big deal because they actively damage wildlife down stream of you. The non-native fish will almost certainly breed outside your pond, and nitrate heavy water will cause algae blooms down stream, killing wildlife and plants just as it would if you had an algae bloom in your own pond. You would need to use only native fish, and test regularly to ensure your fish population (and your feeding habits) don't cause an over abundance of nutrition in the water. Don't forget that most of the fish solids take about 9 months to be converted into nutrients, so a heavy feeding period during spring (breeding time) will lead to a nutrient abundance next winter (when plant absorption is generally lowest).
There are also a host of other more minor problems related to using ponds. The two that come to mind at the moment are visibility and fish management; also problems I have with my 5000 gallon weld-wire tank. Visibility in a pond is going to be terrible. You will have a very difficult time identifying problems before they get out of hand. The problems I am thinking about primarily are disease in your fish, and damage to your pond. Fish management is also difficult because catching fish is so difficult. Unlike with a 600 gallon round tank, you will never be able to catch all the fish in your pond in order to treat an aggressive disease. Unfortunately I have no advice on how to handle these two problems.
If I were to ever use a pond for an aquaponic system, I would either build a weld-wire 'pond' or a man made liner or clay bond in an effort to control the shape to best help me manage the contents. I would avoid anything connected to the local watershed (it should be runoff fed only), and I would make sure it is deep enough to handle evaporation all year, drought years, and an allowance for extra evaporation due to the grow beds. I would stock the pond with native fish (catfish & bluegill in my area) so that if they ever managed to escape the pond, they wouldn't have a significant effect on the local waterways. Feeding of the fish would need to be carefully managed to prevent an overabundance of nutrients, particularly during the rainy season when the pond would overflow. Feeding management will also help control the stocking density of the pond, and all food will eventually be converted into nutrients for the plants. I would put up a 90/95% shade cloth covering the entire pond, along with a low electric fence to keep out most predators. I would pump water from the pond (filtering as necessary to keep out fish & algae) to near by grow beds using a timer to manage the water supplied to the plants if necessary. Grow beds can be any of: fill/drain, wicking, or floating, and they would drain via gravity back into the pond. To manage aeration, I would likely use air lifts, or alternatively waterfalls, fountains, or pond aerators (it churns the water).