I see you are from SC? Have to be careful in warm weather states, even Mid Atlantic. I am taking some photos of how to deal with propagation of water lilies. But the only way to manage them well in a earthen pond that is always full is to keep them in containers. And you have to pull those out and recontainer them every two-three years depending on the size of the containers. The lilies will root, if you take a crown or a rooting piece of rhizome. If you plant them directly in the pond and do not drawdown annually to maintain them they will get out of control.
Freshwater mussels? What a bummer. Shellcrackers might keep the population in check, might. Can only help. I think many of them or different species are on the endangered species list. I know they are in NC. Can't help you there. I assuming the biologist said they were not endangered.
