Marc Okrand, who created the Atlantean language, also created the Vulcan and Klingon languages for the "Star Trek" franchise. Coincidentally, Star Trek (1966) cast member Leonard Nimoy is in this movie as Kida's father, the King of Atlantis.
(at around 1h 25 mins) Jim Varney (Cookie) died just before finishing the film. The "I ain't so good at speechifying" line near the end is the only line not spoken by Varney. Steven Barr did the voice for that scene.
Because the movie was planned out as an action-adventure, the production crew wore t-shirts to work that read "ATLANTIS - Fewer songs, more explosions".
(at around 13 mins) After Milo gets seasick on the first ship, his line, "Carrots? Why are there always carrots? I didn't even eat carrots!" was ad-libbed by Michael J. Fox, who is allergic to carrots.
(at around 1h 25 mins) Vinny mentions that after he opens his flower shop, he'll probably take August off. There's a longstanding tradition in Italian culture that businesses close for the month of August so the owner and their employees and their families can take an extended vacation.