Having big trees around my pond I think I have some experience. I ran into several roots up to 5 inches in diameter from trees that were well over 50 feet tall. Cutting three roots that size that grew into or toward the liner area was not a problem so long as it was done a foot or so closer to the main trunk so any splitting off of new roots would go sideways to the pool. Several of the split offs from the original roots actually encompass the pond. I even incorporated a few to soften the effect of straight sides. No roots try to go through the liner because I positioned any side shoots so they would grow away from the pond or sideways to it.

The recent damage to the ground under the liner, caused by the squirrels housekeeping, was interesting. The areas where the roots were left behind are not compromised. The roots themselves are supporting the liner even though some of the soil there was washed away, causing a slight dip rather than the much larger dips in the areas where there are no roots. The piles of mud from the sides that settled under the liner are all just to one side of the areas where there are no roots.

If you had to remove or redirect more than 20% of the root system, the tree might have a problem but even after 9 years the trees by my pond show no bad effect. In fact there are more leaves than ever. I think it had the effect of what is called root pruning. It stimulates the growth of "hair roots that take up water and nourishment from the soil. Fertilizing with 10-10-10 and watering after a cut is recommended.

Major roots seldom grow more than 5 or six inches in diameter and those that size are supports for the tree. That is why you should leave a good portion behind if possible. Depending on the kind of tree there could be as many as twenty or thirty larger roots going all directions.

Thanks! THis is very helpful!

IF I were to do it all over again I would not have built my biggest pond under the neighbor's evergreen trees. Not because of the roots but because of the constant dropping of debris. Needles, cones, catkins, branches. I don't stress out about them, I simply cannot keep them out of the pond and they don't hurt anything, I had ten year old goldfish until a heron got them but I would not build directly under big trees again. Too much shade for waterlilies....