Lake Jacksonville is owned outright by the City of Jacksonville — the water and the land around it. More than 500 building areas on the shoreline are held on 99-year leases, and a lease transfer requires City Council approval. That single fact changes how a project starts. Before anything gets designed, the lease and the platted lot boundaries have to be established, because the City puts that burden squarely on the lessee: plans for a boathouse, dock or fishing pier must show property corners and lot lines, and the lessee is responsible for accurately locating those platted boundaries before plans are submitted.
From there it is a single-track process. The City Building Official issues the Building Permit for every boathouse, dock, pier and retaining wall on the lake. Construction may not begin until that permit is in hand, and the permit has to be posted in a visible location at the work site before work starts. There is no separate shoreline application and no federal review layered on top for ordinary residential work.
Where a project needs relief from a dimensional rule, the path runs through the Building Official to the seven-member Lake Jacksonville Rules and Regulations Advisory Board, with a $100 application fee and a scheduled hearing. It is worth understanding what that buys: the Board is advisory only, and the City Council is not bound by its recommendation. A variance is a real option on this lake, but it is not a formality, and the schedule needs to allow for it.
Shoretech reads the rules for your specific lot type first — waterfront lease lot, non-shoreline lease lot, or a lot in the Concession Area, which runs on its own looser setback and is the only place on the lake where a habitable structure may be built over the water. What can be drawn follows from that answer, not the other way around.