Bedding media: Hydroton is very popular, but expensive. It is nice to work with, easy on the hands, but some balls will float so you will need to put screens on water outlets.
Expanded shale is also popular and slightly less expensive.
You can use coco-peat, but it will keep your water murky.
Gravel is the easiest and cheapest BUT - you run the risk of getting something in there that will mess with your pH levels - forever. There are tales on the net about people who had to completely empty grow beds and start over because there was something leeching into the water. We are going to use granite which other users are reporting no problems with. What hawkiye said about using slightly larger rock is correct. Pea gravel will work, but you may find the smooth, small stones fit together too well and leave you with oxygenation problems. Whatever you choose, I would recommend getting a bucket, fill it with a sample of the rocks and water, let it sit for a while, then check the pH every day for a week or so, see if it stays stable. You can adjust it up or down, but if it just keeps leeching you will want to pick different rock.
For a pond that big, I would look very hard at tilapia. They gill-feed, which means the filter the water through the gills and eat the algae. That means cleaner ponds, and less food you have to provide. It also means if something happens and you cannot feed for a day or two, they will live. The down side... Check with your Fish and Game people, they are considered "invasive" in some areas and you are are not supposed to put them in ponds. Also, if you live where it freezes, they will not make it through the winter. What we will do is raise them from fry starting late winter, harvest most of them in early winter, and put a breeding set into our greenhouse each year.
I agree again with hawkiye, that you may have a problem with nutrient density. Tilapia breed readily, so again, they might get you fishified fastest. Any other critters you can add to the system will help - crayfish, shrimp, goldfish, whatever you can get for free or cheap.
You will hear a lot about "cycling the system" and your ducks will fix that for you. You need a bacteria in the system to convert ammonia to nitrogen, and the duck poo will provide it. If you can, get the ducks at least a week or two before you use the water for your grow beds it give the bacteria plenty of time to colonize.
I want to see your video when you get this going - it sounds like an amazing project! If you want to, PM me and I will email you our phone number, and you can call with questions... We might even have answers for you.
You can daisy chain the beds together. We did find that the last bed got much less nutrient than the first bed, so you may find you want to make adjustments if your end of the line beds look puny.
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