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.

One issue that has always plagued Valheim ships is that the raising and lowering of waves suddenly, causes damage to ships, and is especially more evident during times when the player sleeps to pass time... The boat raises up with the high wave but then the water drops out suddenly, and the ship "falls" a short distance to land in the water, and that's what causes the damage.

Enough times of this smaller "fall" damage, and the boat breaks apart.

To keep your ship safe during long periods of not using it, manually break down your ship, in SHALLOW water, to retrieve all of your materials back, and simply re-craft a new one as needed.

Originally posted by Gladi8er65:

One issue that has always plagued Valheim ships is that the raising and lowering of waves suddenly, causes damage to ships, and is especially more evident during times when the player sleeps to pass time... The boat raises up with the high wave but then the water drops out suddenly, and the ship "falls" a short distance to land in the water, and that's what causes the damage.

Enough times of this smaller "fall" damage, and the boat breaks apart.

To keep your ship safe during long periods of not using it, manually break down your ship, in SHALLOW water, to retrieve all of your materials back, and simply re-craft a new one as needed.

I know it used to. I still hear the sounds. However I have yet to see any damage inflicted on my longship in the picture.

Those are beautiful harbors, looks like a lot of work went into those.

I only just started playing again recently but I remember losing boats no matter how hard I tried. There would always be a mob that somehow worked its way through walls, defences, etc., and smashed the boat. I used to disassemble them too for the sake of not losing materials.

To try and prevent that I am using Cheb's Necromancy mod (there's a Mercenary mod by the same author, where you can hire people for gold) and when I get around to building a boat I'll station some warriors and archers who will kill off sneaky mobs for me. I'm also toying with the idea of using the Steamheim Airships mod, but it seems a bit "techy" given the Viking theme. Maybe after I've played for a few more weeks, just for fun.

Originally posted by Emelio Lizardo:

Originally posted by knighttemplar1960:

... If it is within rendering distance while you are playing creatures can spawn near enough to attack it without you knowing that they are doing so.

Like, right in the 'harbor', or just outside the walls?

Rendering distance is the distance from you that the game program is active (64 tiles). Nothing happens outside rendering distance but you can't see all the way out to maximum rendering distance either. That means that things can spawn outside your visual radius (unless you have a large enough workbench/base structure radius) and still affect things inside rendering distance.

Originally posted by Emelio Lizardo:

I took the walls out into the water as far as it would let me. My solution so far is simply to disassemble the boat when not in use.

The earthen walls are indestructible your boat isn't. Building your pier out of earthen walls instead of wood may be your problem. Wave motion inside rendering distance that causes your boat to brush against your earthen walls can destroy the boat slowly over time as can boulders under the water. Dismantling the boat after sailing is all most always the best option.

I think I've not lost a single boat(!) in >1000h of playtime (2500-3000 in-game days).
One raft in a swamp outside a crypt, yes - but no boats.
Some got destroyed by enemies but there's always a workbench nearby to protect the dropped materials from de-spawning.

https://steamcommunity.com/sharedfiles/filedetails/?id=2972766552
https://steamcommunity.com/sharedfiles/filedetails/?id=2972766521
The current slightly larger version of that dock ^^ works fine too.
And waves go at least +/-3m (6m) at that location.
Meadows is much safer - don't see large waves at shallow shores there.

https://steamcommunity.com/sharedfiles/filedetails/?id=2972560018

Originally posted by knighttemplar1960:

... If it is within rendering distance while you are playing creatures can spawn near enough to attack it without you knowing that they are doing so.

Like, right in the 'harbor', or just outside the walls?

I took the walls out into the water as far as it would let me. My solution so far is simply to disassemble the boat when not in use.

I agree. Breaking down the boat at the end of the route is the best idea. Otherwise, you risk losing the nails, and other parts.

Monsters will swim a dozen miles around your walls to smash a boat, they hate boats THAT much. Building a gated harbor is a fairly difficult project. Storm proofing is nearly impossible because water follows global behavior and you can't block out the massive storm surges that smash boats in harbor.

The safest boat harbor is storing the raw parts in a box.

its totally possible to build a completly safe harbor. monsters only go for boats they have a line of sight towards.

you can either dig inland to reduce the waves or find a natural inland bay to start working on for it.

https://steamuserimages-a.akamaihd.net/ugc/2023848732779197312/E5B5EDB317E9568914C7B340F1C3C2F46383E577/?imw=5000&imh=5000&ima=fit&impolicy=Letterbox&imcolor=%23000000&letterbox=false

Yes, but you have to check on it and make repairs to it from time to time. Without a roof it will suffer weathering damage down to 50% health. If it is within rendering distance while you are playing creatures can spawn near enough to attack it without you knowing that they are doing so.
https://steamcommunity.com/sharedfiles/filedetails/?id=2948948712

I usually raise land up to form a couple of piers.