Some filming for this movie took place on an actual WWII submarine. The USS Silversides (which is available for tours) located in Muskegon, Michigan, was towed out into the middle of Lake Michigan where scenes with Bruce Greenwood were filmed. The Silversides had some minor re-painting done (rust coloration) but is now back to her original gray color. The rest of the sets and models used in this movie were all based on the look and layout of the Silversides.
Darren Aronofsky, who co-wrote the screenplay, was originally going to direct the film in 1999 but instead made Requiem for a Dream (2000).
Originally Frank Sinatra singing "I'll Be Seeing You" was supposed to be mysteriously playing on the record player. When the studio had difficulties obtaining the rights, the song was replaced by Benny Goodman's "Sing Sing Sing (With a Swing)".
Holt McCallany learned how to do several yo-yo tricks for his character Loomis. Some of the tricks he performs in the film are the Brain Twister, Around the World, and Walk the Dog. His instructor, Brian Cabildo, is listed in the final credits.
When Darren Aronofsky was supposed to helm the film, it was a straight horror thriller called "Proteus".