We've used bags & bags of bentonite in our 1/2 acre pond trying to find a leak! The leak isn't as bad as it used to be! The nearby farmer uses it in his ditch (runs through the mountains for about 3 miles) to slow down the leakage. It works to a degree, but the ditch still leaks enough underground down the hillside to fill up several ponds on our property!
The main drawback that I have read and heard about is leakage. A fluctuation in depth will cause the clay to dry out around the edge of a pond. The clay shrinks in the drying process and more water is lost. So, unless you have a fresh water supply like a stream or an automatic filler you will have a constant water loss problem. The roots of uncontained water plants will penetrate the clay, causing even more water loss. In a large field pond the surrounding area is used as a watershed to refill the pond. In most garden ponds we try and prevent rain runoff from entering the pond because it contains pesticides and fertilizers from the neighboring yards.
On a more positive note; bentonite is suppose to be very good for your fish. It promotes good health and enhances color intensity.
Not an expert, just sorta parroting what Iíve heard!