Originally posted by Luward:

If you are playing on Windows, you can hold Shift to change between the ground under you or the ground where you are aiming. The Linux version is bugged and the hoe does not function correctly.

Originally posted by wizard_of_woz:

If you are swimming, then a baot will be able to go there.

If the wind picks up and you get deep troughs in the waves, the boat will be destroyed from constantly hitting the ground.

I've noticed that the high waves from storms don't go very far into bays and rivers. so if the OP is builing in a small bay thats already deep enough to almost swim in their ships might be safe in even the worst weather. Just going by a verbal descriptions its hard to really know about it's geography.