I have a 12 year old pond 14ft in the deepest area and shallow areas through out I tried planting eel grass and American pond weed but it does not take. I planted pond lily and they have taken but something comes by in late spring and cuts the leaves off. The pond has a clay bottom with the shallows from 1 to 5ft tapering off and then a steep drop. Any one have a clue as to why plants won't grow but WLs will ?

aphids can eat leaves above water, crawdads can eat any and all below water. CAN, doesn't mean they are but that is one possibility.
Nutrient content and water chemistry can play a role also.

Underwater plants need sunlight to get to the bottom of the pond where they grow. If you have TGC in the pond they could be the problem. Crayfish could also be a problem. Geese/ducks can also be the reason why you can't get the plants established. Turtles or possibly muskrats could be the issue with the WL getting the leaves cut off.

Thanks for the reply but unsure what you mean by TGC

TGC = triploid grass carp (sterile)

There are certain plants that they are quite adept at eating.

Some light reading for you. https://forums.pondboss.com/ubbthreads.php?ubb=showflat&Number=92442#Post92442

Turtles can and will decimate both eel grass and pond weed. They can also eat water lilies to destruction.

I have successfully use branches from thorny honey locust over newly planted aquatic and marginal plants to protect them, but handle with care because the thorns are wicked. Nice thing is that unlike fencing, the branches eventually rot away. Good luck!

Turtles will eat lilies and eel grass out of existence. I fight them constantly and cage everything I plant. American waterlily,,once established and large, can stand up to them. Illinois pond weed gets wiped out too if not caged. They don't touch alligator weed unfortunately.