Taken from seaplanes.org:
While most pilots assume the FAA has jurisdiction over landing areas, including water-based landing areas, the truth is much more complex. Jurisdiction rests with the person or organization that "owns" the waterway. This may be a Federal or state agency, a local government, a private corporation, or an individual. Determining who controls a waterway is the first step in determining whether it is legal to land on that body of water.
A second complication enters in the picture with overriding jurisdictions, most commonly state-imposed seaplane base licensing requirements. In several states, notably Ohio, New Jersey and Indiana, seaplanes may not land unless the proposed landing area is certified as a seaplane base, regardless of whether the waterway owner provides permission or not. To determine whether this is an issue in your area, call your state aeronautics office (often a division of the state department of transportation), check the Water Landing Directory, or call SPA Headquarters (863/701-7979).