Sometimes neighborhoods wil have covenants that will control what materials you can use, the house type ect. These are not zoning restrictions. Those are another layer over a covenant. You mention waterfront property. Many times there are very strict restrictions controlling development in a flood plain/flood fringe area. Make sure that you understand these restrictions fully. To develop a piece of property in a flood fringe area can result in thousands of dollars in engineering fees. Not to mention additional building costs.
I believe that Wisconsin requires the ENTIRE pier to be removed. Naturally, you state will be different. Check into it.
I think that Fred offered some good advice about contacting an attorney. He will know what to research and will have experience in the area. It will proably cost you alot of money initally, but you may save a bad investment in the long run.
FYI-Becase the property doesn't have an improvement on it (ie structure) it will be tough to get a loan to purchase the property. You may end up paying cash for it. Having that much cash invested into the property may leave you short handed when it comes time to get a construction loan. Be sure to look into that aspect.