The Dark Dweller, master of the Dark Water, was an evil being that resided within the Chamber of Lost Souls at the center of Mer, where the evil liquid is spawned. The Dark Dweller himself seems to be made of Dark Water, implying that the Dark Water is not so much under his control, but a part of him and an extension of his horrible will (either that, or he is an evil spirit who inhabits the Dark Water and can bend it to his will).
The Dark Dweller seems to keep to himself, content to let his minions, Morpho and the Dark Disciples, and the Dark Water itself do his work for him. It was mentioned by Bloth at one point, however, that sometimes sailors could see the Dark Dweller's face reflected in the surface of patches of Dark Water, and that to see it was a bad omen.
Originally, both he and the Dark Water were trapped in their domain by the seal of the Thirteen Treasures of Rule, but after a time the Dark Dweller became powerful enough to cause a rift in the ocean bed, allowing the Dark Water to begin seeping out, thus beginning the Year of the Black Tide. He then sent Kiroptus to scatter the Thirteen Treasures across Mer, so that nothing could stop him from enveloping all of the world in the Dark Water.
When Tula fell into some Dark Water and was sucked down into it, the Dark Dweller spared her life, keeping her alive in his domain so that he could use her ecomantic powers to lure Ren there, in the hopes of stealing the first seven Treasures of Rule. He took on Tula's form in an effort to persuade Ren to give him the treasures, but his treachery was revealed when "Tula" didn't know exactly where Ren kept them (they were in his pouch).
He then tried to make a bargain with Ren: one treasure in exchange for Primus' soul. But, like Tula, this "Primus" was merely the Dark Dweller in another form, and Ren drove the monster away with the combined powers of the seven treasures. Weakened severely, the Dark Dweller was forced from then on to rely entirely on Morpho and the Dark Disciples to get his loathsome work carried out.
The Dark Dweller returns as the final boss to the Genesis game. After collecting all the treasures, the Wraith's crew confront the Dark Dweller in a cave near Dragon's Maw. After a fight Ren uses his compass, now empowered by the treasures, to fire a beam at the Dark Dweller. This beam seals the Dark Dweller within a renewed Six Seals, ending the Dark Water's threat to Mer.