Once upon a time (not a fairy tale ) when I first learned timber frame deconstruction in the finger lakes (circa 1950) I observed several very old boat house underwater foundations which had lasted some time. The cribs were bolted together with about 1 foot extending from each corner to provide a right angle pocket around a pole driven in the lake bottom. The remaining center space inside the crib was(about 6' square) filled with large rock (1 cu ft or larger).The crib top was typically 3' above the mean water level. Walkway docks were then placed on the cribs on which the boathouse was built.
Based on the experience of the wooden submerged timbers used on the St Lawrence waterway they are of red oak and replaced at nominal 30 year intervals. These timbers can be dried and used in a new above ground timberframe. The problem of submerging wooden timbers is finding a preservative the environmentalists will let you use not withstanding any provisions of NYS law/building codes.
Good luck and work safe.