(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.
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.
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.
The written Atlantean language is to be read left to right, drop down a line, and read right to left, continuing this cycle. It was done to create a flowing, water-like movement reminiscent of the Atlantean culture.