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Concerning the roots. Maybe you can cover that area with something ridgid. Maybe plywood or there's a flooring product that is cement based that is called hardy backer board. It will probably outlast plywood. You can buy it in various thicknesses at hardware stores, Home Depot or Lowe's.
Then a layer of carpet, carpet padding or underlayment. I would make sure I cover the area well beyond where the roots are at this time. They will probably spread out once they hit the board.
I like this idea....but at the same time Im intrigued by this post by Waterbug
Pond liners vs roots
Pond newbie here. Please be gentle. I read a book on koi keeping and decided to dig a small pond planning to use a 45 mil liner. However, the area I want to put the pond was formerly a planter. As I dug, I am concerned about the roots from the former plants and/or plants that are outside...
www.koiphen.com
It certainly couldnt hurt putting up a wall of that backer board (decently priced at home depot) if for nothing else then piece of mind. I just really wonder if its needed. Hmmmmm