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How deep will your deep vs shallow shelves be? That's something I haven't decided on for my own pond.
I didn't think of using clay based soil.... I have to dig a new hole for the bigger skimmer I picked up, and will be digging into pretty much straight clay (UGH), so maybe I'll use that with some aquarium gravel... Caribsea makes substrate but it's 20 bucks for a 20 pound bag, which would only fill about half a pot...I'm hoping that just having the pump (Danner/Pondmaster Proline 2700) sending the water through the waterfall weir, which has a filter pad and bioballs, will be adequate. The guy at the pond store didn't seem concerned with that design. I really didn't want the expense and complication of having a skimmer since I planned on lots of floaters, but I guess I will see over time if I made the right decision.
I have a variety of depths: 12 inches-20 inches for the high ledges. I didn't really plan for them to be 20 inches deep, but when I put the laser level on the shoreline, it was obvious that I need to raise the lower pond edge up quite a bit; but I was too lazy to go back and raise the low spots on ledge. ~24 inches for the deepest part of the shallow end. ~36 inches for the deep lily shelves and 48 inches for the bottom of the deep end. It makes a nice stairway for me to get to all the levels. Those depths I hope will be good for the plants I plan on. I have many of them currently raised up on overturned pots since those are the recommended "mature" depths and, of course, all of my plants are newly potted.
I don't know exactly what soil was used for the plants I bought pre-potted in non-mesh/non-draining pots, but from the weight and color of soil that seeped out when I soaked them, it appears to have quite a bit of clay. They are topped with small gravel. The pond shop here will split/replant your overgrown pots including all the soil, new pot and gravel for just a few dollars a piece. For the plants that I got from the lake, I lined plastic mesh Laguna pond pots with landscape fabric and then put the plants in lake muck - which again in this area is very clay based. I topped with about 1 inch of small gravel. I have read that some are recommending just putting the plants in only gravel, with no soil at all. I might try a few that way to compare how they grow vs. the clay based approach.