Step 1 Water Depth
Make the area deep enough to get the boat in, but you can still loot items from the floor.
You can do this by using your hoe. When you use a hoe it bring the ground up to the level you are currently standing over (even if on a boat, platform, etc.) This way if your boat is destroyed you can get the materials back.

Step 2 Workbench
You need to make sure wherever you park your boat has a protected workbench. Protected meaning mobs cannot get to it to destroy it. They can destroy it first and then the boat. The best way to do this it "bury" your worktable (but not with a hoe) by digging a small pit then going over the top of it. If you do not do this then a destroyed boat is subject to the timer before the items despawn.

Drifting
You kind of want to put bumpers in on your docks to keep the boat in place. Like a U shape or so. Otherwise the bigger waves will make your boat drift out to sea. I think I seen some use actual gates before.

Waves
It does not matter how deep your harbor is the waves get big enough they will still make the water level go up and down ten feet at some times.

Swimming mobs
Mobs will swim around walls and such to get to your boats, so it is best to do the two steps above to ensure not losing the boat or the cargo.

https://steamcommunity.com/sharedfiles/filedetails/?id=2972998088
This was kind of a pain to get the dock in because since the mountains are so close to shore the water gets really deep fast.