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Ive looked at online mas for harbor locations as I only have two on an island and novigrad. I ve been to all the places in velen and novigrad where the other harbors should be but they do not appear on the map at all. Anybody else experience a problem with harbors not appearing on the map?

What exactly is your problem? A harbour is simply a coastal area of shelter. It does not have to have structures. Is this what you are referring to... structures?

Harbor icons only appear on your map once you are in a boat and sailing. Note that just entering a boat and taking the helm doesn't count.

Harbors are fast travel points - only for boats.
Anchor symbol=Harbor=fast travel at sea.
Nice and easy.

Never used it.

Bummer. It's pretty darned convenient, considering how many boats there are lying around.

:) not using an option does not mean that there is no option.

Used it a lot after sirens went away from my vessel with large chunks of the boat removed.
On skellige there are enough harbors to get to and from each island free of any stress (and once on land: poor sirens!).

Yeah, but I've sailed all around the Skellige isles without having to break immersion, and 'teleport' out of danger, or to another place. When I spy sirens, I dive in; they dive in; crossbow removes sirens; I get back in boat. Simple.

... made it a habit to bath only once a month (in game).
Never heard it : "... did you wash your hair recently?" from bystanders in Novigrad and about.
Harbors are a healthy thing, nothing to do with "immersion".
For the crossbow under water -- give me a harpoon and things are set.

And, you are not "teleporting" out of danger - quite the contrary, you go highspeed to the next encounter of your questing life, not some meaningless slaughter of minor airborne things (nice tits, though).

You need to stay off the hard stuff.

I would like to blame Zoltan for that...

Hmmm. I bet.

Yea my problem is the harbor icons dont appear even when sailign around. I have a grand total of 2 in the hwole game though ive explored pretty much all of velen and novigrand and am well int o skellige now. It would make sailing around skellige a bit less painful for me if i could fast travel from boats.

Don't know if it can be any help, but here

http://witcher3map.com/

you'll find maps, icons and small descriptions of each "point". Harbors included.
Are you quite sure that you have not disabled one or more things in the filter section of your maps (in game)?
Velen/Novigrad combined should have eleven harbors, Skellige has seventeen harbors.
Could understand if there are no harbor icons at all, but two in total?