as the above player write.
I build a wood wall around my harbour and a bit out into the water. and there is also a workbench there where the radius cover the ship. So far this method work really good.
My ship is parked in an area with deep water.. It wont protect against attacks but i think it help a bit with amount of creatues want to go there since normaly most animals do not walk further out into the water than shallow water, many wont go out into the deep water exept if they hunt something.