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Ditto on the clay/bentonite where the stumps are (once they are removed). When they rot away they are going to leave a hole in the bottom anyway, and when the roots rot away the water can follow where they were to leak out of the pond.

I'd get some heavy equipment in there (even a backhoe), remove 'em and pack the holes that are left.

Next year, if you have an algae problem, look into stocking Blue Tilapia. That'll take care of the FA problem. They'll have to be restocked yearly because they won't overwinter.