Years ago, I built at 37' x 25' x [0.0 to 5'] garden pond using 45mil epdm liner. I only recently saw a catalogue of excellent bentonite clay-built ponds and now regret having used liner - or so I think, pending responses on this forum.

The down-sides to using synthetic liner (vs clay):
*Difficulty of repair should a tear occur - including from tree branches falling in.
*A terminal life-span; may not last a full life-time, in case that matters to you
*There is a potential that moles/voles and other ground-rodents may bore into the liner. Underlay - such as carpeting, I suppose, would have to be adequate. Tree roots may also piece the liner; not sure if this is also so of clay-based ponds.
*You cannot plant things like cattail (Typha spp.), or other plant species which would puncture the liner; I'm not sure if this is still the case when it comes to clay-built ponds, however.
*Any exposed area will reveal rubber, instead of a natural looking substrate: clay; you'll need more stone coverage to conceal the entire surface of the rubber - which may be an issue for those not wanting stone in their pond, due to maintenance issues. You'll also need the stone to conceal all of the unnatural creases.
*For complicated designed, you will need to purchase far more liner then necessary.
*For very large liners, there is difficulty in installation - I'd rather deal with the clay-pond challenges.

So, I'm thinking of dumping my pond, cutting away all of the liner (leaving the bottom drain in place), and removing all of the underlay (carpet) and going with sodium bentonite.

These are my concerns:
1. Will tree and shrub roots (particularly wetland species - i.e. willow, blackgum, and birch, etc.) penetrate the bentonite, being in search of water? There's no way I'm doing away with the awesome wetland plants I planted in my mesic soil around my pond - natives: sweetbay magnolia; paper birch; blackgum; common button bush; various shrub dogwood spp.; coastal sweet-pepper bush; silky willow; highbush blueberries; American black elderberry; and thicket-serviceberry. If so, I'd rather stick with liner.

2. After rain-storms, my water-table rises. For instance, if you dug a 5' deep pit in the yard during a dry month, there is no water; after it rains, there is water to the top. Excavating the pond confirmed this. Wouldn't the groundwater pressure (which would cause the rubber liner to lift if I were to drain the pond lower than half-way, as it is) cause the clay-seal to rupture?

3. I actually have a yellowish clay once you dig about 2' down. It is not impenetrable, but I guess it would be a little bit of extra protection, beyond the standard depth of applied bentonite clay. Do I have the proper conditions enabling me to build a clay pond?

4. Can I plant emergent aquatics with deep, penetrating roots in a clay pond? Plants like: cattail and common buttonbush?

Thank you,
Steve

Let me answer some of your concerns.
If you have a tree branch that is large enough to tear the liner in the pond will also tear up the clay. In each case they both will leak. The liner can be repaired usually fairly easily. That is also true of the clay.
The liner has a life span of about 50 years.
Yes animals can chew a hole in the liner but far less likely than with a clay pond. You won't have a problem with either moles or voles. You can have a problem with chipmunks and mice at the surface of the pond or muskrats below the water level. But the liner will be easier to repair in any case.
I have had cattails planted in liner ponds for 20 years and they have never put a hole in the liner. With clay they would not have a problem growing through the clay.
For the most part any unnatural creases will disappear once algae starts to grow.
Yes there can be some waste with liner ponds and liner can be heavy.
I would say that all these things came from the website that was trying to sell you on clay. They told you some of the downsides of a liner pond but not the down sides of a clay bottom pond.
Almost all clay ponds leak. It is just a question of how much. Clay ponds are almost never as clear as a liner pond. Any roots can grow though the clay. You talk about ground water lifting the liner. If you have a clay pond that is totally sealed the ground water will lift the clay until it leaks ground water in. Once that happens when the ground water goes down the clay will continue to leak the liner won't. Getting debri out of a clay pond is a pain. This is just a few of the problems with clay ponds. There are more and I won't go into them here. There is a reason why most smaller ponds a liner and not clay.
Mike