Due to the good ratings this show received, the producers of this show decided to extend the adventures by finding fewer treasures per season compared to first and second seasons. While working on the third season (episode "The Dark Disciples" to "The Living Treasure"), Fil-Cartoons (Overseas Animation studio) had some difficulties with animating the last four episodes (episode "The Pandawa Plague" - "The Living Treasure") of this show. This caused problems for Hanna-Barbera animation studio, because the episodes were coming in late. This prevented the show from meeting the air dates. This led to the cancellation of the show in November and December 1992. The last four episodes were finished, and aired six months later (May 1993). But by that time, most of the crew of this show were already in the middle of the production of Swat Kats: The Radical Squadron (1993), and Cos Anzilotti (Producer of this show's third season) was already in the middle of the production of Captain Planet and the Planeteers (1990). Due to the failing of meeting the air dates, Jayne Barbera was replaced by Catherine Winder as "Executive in Charge of Production" for later Hanna-Barbera shows like Swat Kats: The Radical Squadron (1993) and 2 Stupid Dogs (1993).

One of the few Saturday morning cartoons that actually show two characters dying. In the episode "Break Up", while Ioz and Tula are fleeing from the guards during a revolt, on Pandawa, one of the guards falls into the water, and the Dark Water engulfs him. In the episode "A Drop of Darkness", an old woman named Cray tries to make a youth potion. However, it doesn't turn out too well, the potion actually ages her to the point she becomes old, and dies.

This show was originally released as "Dark Water". But after five episodes, executives at Hanna-Barbera (owned by Ted Turner at that time) decided to make the show less serious. So from episode six, "Andorus", onwards, the show became known as Pirates of Dark Water, and less serious, compared to the first five episodes.

Roddy McDowall voiced Niddler for the first five episodes. He was replaced by Frank Welker.

Glenn Leopold used the body switching idea in the episode "The Soul Stealer" again in The Real Adventures of Jonny Quest (1996) episode "Cyberswitch".

After the first five episodes, Roddy McDowall requested a higher salary for his role of Niddler. But the studio denied his request. So he quit and left the production, and Frank Welker (who did squawking voices for Niddler) took over for the voice of Niddler.

In the original version of the episode "Victory", the final scene was different. The episode only had Tula and Ioz with Ren. But, in the later released versions, additional scenes were added, where Niddler and Teron joins with Ren, Ioz, and Tula in the end.

In the Warner Brothers DVD version of this show, the ending credits for the first episode and the third episode are incorrect. For the first episode, the ending credits are supposed to be with an octopus on the background. In the end credits of the first episode, the writers of that episode should be listed as Kelly Ward, Mark Young, and Flint Dille. In the end credits of the third episode, the writers should be listed as Lane Raichert and Mark Young.

Many voice actors and actresses, who worked on this show, also worked on The Smurfs (1981). Frank Welker (who voiced Hefty Smurf, Peewit, Poet Smurf, and other characters) played Niddler, Kerroptus, The Dark Dweller, Morpho, and several characters on this show. Linda Gary (who voiced Dame Barbara and other guest voices on The Smurfs) played Jenna on this show. Brock Peters (who played guest voices on The Smurfs) played Bloth on this show. Hamilton Camp (Greedy Smurf on The Smurfs) played Roulette on this show. Michael Bell (who voiced Handy Smurf, Lazy Smurf, Grouchy Smurf, and other characters on The Smurfs) played Swar, Ratmore, and Grollis on this show. Keene Curtis (who voiced Balthazar on The Smurfs) played Keron the Wizard on this show. Andre Stojka (who voiced guest voices on The Smurfs) played Slaggon and Joat on this show. Peter Cullen (who voiced "Great Book of Spells" and other characters on The Smurfs) played Mantus on this show.

Frank Welker played Niddler similarly to the character "Peewit" he played in The Smurfs (1981).

Although Niddler was originally voiced by Roddy McDowall, still the squawking sounds of Niddler was voiced by Frank Welker.