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Skullport is Located in level 3 of Dungeon of the Mad Mage DotMM beneath Waterdeep.

Now that the party has repaired the locks, the port can be accessed through a tunnel in the cliffs. In a few months the local economy will rebound and the masters of the dark market (including Xanathar and the Zhentarim) will be beholden to the party.

There is probably a secret exit from the Fountain of Ngalish here somewhere amongst the highest cobwebs of abandoned netting.