According to
These guys , you want to mix the bentonite with native soil, not have a solid layer of bentonite:
"How Much Bentonite to Seal a Pond?
In the bottom of a 5-gallon plastic pail, drill 20 to 25 eighth inch holes. Gather enough soil from the area to be sealed to fill about 3 inches of the pail. You can either select the most porous soil, (sand) or a mixture of soil taken from several areas of concern in order to present an “average” soil.
In this soil, mix one to two pounds of bentonite and tamp down in the bottom of the pail. Into this pour a gallon or two of water and see if the bentonite provides the necessary seal. If not, repeat the process and increase the amount of bentonite by half a pound until the water is contained within the pail.
The bottom of the pail represents about one square foot. When you know how many pounds of bentonite it takes to seal the pail, then we know how many pounds per square foot to distribute and roto-till into the pond, dam or other earthen structure. "
I would plants in the way nature does it: put them in directly in, no containers. The point of a container is to control growth of plants and to keep the pond "clean", which is more in line with an ornamental pond, not a pond you want to naturalize.
As for ducks, as far as I know, they are not clean freaks so they should be fine with the water being a bit murky until the suspended particles in the water precipitate out.
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