Plant your lillies in water soil in wide Pots or containers and 6 inches deep then cover with pepples. The ducks won't be able to eat the lillies, but they will eat the leaves and flowers.
If you use some metal stakes or wood you can create a little fenced in area in the pond. This will protect the main plants and only let the ducks get to the edges.
Be careful what materials you use for the fence - no sharp edges or you can injure the ducks.
Google water lillies and duck ponds. There are a lot of helpful sites