Dark Water is slowly taking over the world of Mer. With his last words, King Primus tells his son, Prince Ren, that he has to find the lost Treasures of Rule to stop the Dark Water. Ren travels to the town of Janda where he meets the monkeybird Niddler, the female warrior Tula and the ex-pirate Ioz, who help him on his quest.

Based on the cartoon by the same name, The Pirates of Dark Water is a side scrolling hack'n slash platformer with a few adventure elements.

You take control of either Ren, Ioz or Tula who can jump, climb, attack and throw enemies. In most levels you are required to find keys to unlock doors and talk to NPCs who will give you hints. You will also find numerous useful items including throwing weapons, food to replenish your health, potions that have different effects such as temporary invincibility, money that is needed to pay certain NPCs and melons that can be fed to Niddler who will take you back to the map screen in turn.