Running a channel, where the water level is always flat (no waves) and isn't affected by storms, wind, or tide, you could get away with only being about 1 meter deep. The deck you see when looking at the boat is literally the bottom of the model and the lowest point considered for whether water is deep enough to run through (though karves and longships have cargo compartments under their decks, these only exist in a purely abstract sense).

Once you start getting out to the endpoints where tides and waves and all that other fun stuff starts having an effect, then you'll want to start digging to as low as 3 meters below "shoreline" (where beach sand gives way to grass) to keep the mouth navigable during night storms. Generally, for those areas, you'll want to start working during a storm and keep picking away any time you're in a low point of a wave until you just can't pick any more.

Originally posted by Pyro Penguin:

i dont think thats right, its just that eventually the land becomes too high above water level and you cant dig down far enough to reach it

Correct. You can only dig land down a maximum of 8 meters from where it was originally generated (and Raise Ground has an 8 meter limit up), so any spot that started out 8 meters or more above shoreline is never going to be able to touch water (without a certain mod at least, but that one absolutely requires that the server and everyone that plays on that map use it or the whole map can become messed up).