I recently purchased a 5/6 acre farm pond. It has a large area (about 2 acres) that is 1 to 3 feet deep, with the rest of the pond droping off to a maximum depth of 11 feet. The pond is spring fed from the shallow end, with a pipe out flow at the deep end. This pond is in sothern PA.

I am thinking about planting water lilies in the shallow end of the pond. We have muskrats and a healthy fish population. I thought the lilies would be good for both. I am worried about the lilies "taking over" and completly covering the whole pond. If planted, would they stay in the shallow end? Are there any specific plant types that will not grow in deeper water?

Yes, in an earth bottom pond, water lilies can take over up to a depth of about 5 feet or maybe more. Most water lilies like to be in water less than 3 feet deep though so I doubt the entire pond would become covered. Muskrats will eat some water lilies. I have a book on beavers where one group of them lived on nothing but water lily rhizomes. There are so many kinds of aquatic plants! My plant lists are at http://www.fishpondinfo.com/hardy.htm and list preferred planting depths of many marginals. Some plants grow faster than others. It really depends on what you had in mind for the plants - filtration, food for certain animals, pretty color flowers, nice foliage, tall or short, etc. I suggest sticking with native plants.

I agree with your comment about native plants. I thought water lilies were native to the eastern USA. Am I wrong?

There are native water lilies but some aren't. Obviously, the tropical ones aren't. I think a lot of the modern hardy water lilies were derived from native species but aren't "natural" since they were developed by people. The native water lily has a medium-sized yellow flower I think. I would consider most hardy varieties of water lily "native" enough to use in a native pond.