Birds, mammals, contamination in stocking water are all possible options. I am betting birds are the most likely candidate though.
Take some quality photos and post them on here. We can help you ID what you got.
Spot treating the lily pads with a liquid glyphosate formulation can be moderately effective on most water lily species. Glyphosate isa broad spectrum, systemic herbicide. Systemic herbicides are absorbed and move within the plant to the site of action. An aquatically registered surfactant will have to be added for good results.
A less selective option(it will kill other plants in the treatment area) but the most effective are 2,4-D compounds. 2,4-D compounds are also systemic herbicides. Instead of being a liquid that is applied to the leaf surface, it is in a granular form and spread over the water surface sinking to the bottom. There, the plants absorb the herbicide and die.
