Is there anyway you could give us a picture of what this looks like now? I still am not understanding about the tree.
Your demensions (as of now) are (in my terms because I can't visulize meters

) 16.4 ft x 4.92 ft x 1.64 ft you said this was disapointing and I think it was the depth you were disapointed in? Why not dig a little deeper then, or maybe there is a reason you can't go deeper? I would say another foot and a half would be a lot better. With the dimensions you have now your pond is 958 gallons or 3,625 liters.
On the tree, here is what I did with my tree. The trunk of the tree is only about 2 feet from the edge of the pond. This first picture is of the building stage, but it shows you really well how close the tree is to the pond (tree is at top of the picture with landscaping bricks).

this next picture the pond has water in it, you can see the tree on the right side of the picture with the bricks. The water level can go over 1 1/2 bricks when the pond is full. It looks really cool in person, hard to see on a picture.

This may be a good option for you? Again though I am not exactly sure how to picture your tree. If the tree is in the middle of where you want your pond maybe you should build two ponds one on either side and put a stream going from one to the other. You could take the dirt from one of the ponds to build up around the other and have a water fall coming from the higher pond down to the stream and the stream to the second pond (where you got the dirt from)? I designed my pond, and I think I'm pretty good at this

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The roots of your tree should take the course of least resistance. Remember they are tiny fragile roots as they grow out, they do get bigger but those tiny little roots that find the new paths shouldn't poke into your liner. They should follow down and along your liner. At least this is the way it was explained to me. Someone on koivet.com posted a picture of their pond with a huge spruce tree almost on top of it. They said that the roots have never poked into the liner. My tree is a box elder and thus far no troubles. It's only been in the ground for two years, going on three. It's has grown four times faster than a normal box elder would, but I did have water running out of my upper pond constantly watering it until I finally figured out where the leak was! LOL
Good luck with the pond though, pictures would be great! please

Scott